List of works - Takashi Kumasaka

A calcium-dependent xylan-binding domain of alkaline xylanase from alkaliphilic Bacillus sp. strain 41M-1

scientific article published on 07 February 2011

A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals

scientific article published on October 2013

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.

scientific article published on 14 July 2017

A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate.

scientific article

A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method

scientific article published on 14 June 2019

Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

scientific article

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

scientific article published on 17 October 2019

Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals

scientific article published on 21 March 2018

Assembly of homogeneous norovirus-like particles accomplished by amino acid substitution.

scientific article published on 29 June 2011

Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8.

scientific article published on 14 April 2005

Characterization of Nocardiopsis beta-1,3-glucanase with additional carbohydrate-binding domains

scientific article published on 01 January 2007

Cloning and functional characterization of the copper/zinc superoxide dismutase gene from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6

article

Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme

scientific article published in January 2003

Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals

scientific article published on 25 November 2020

Contribution of salt bridges to alkaliphily of Bacillus alkaline xylanase

scientific article published on 01 January 2007

Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus

scientific article published on 28 June 2017

Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor

scientific article

Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

scientific article

Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

scientific article published on 13 January 2017

Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel

scientific article

Crystal structure of rhodopsin: A G protein-coupled receptor

scientific article

Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor

scientific article (publication date: 23 May 2003)

Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis

scientific article

Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii

scientific article

Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants

scientific article

Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics.

scientific article

Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain

scientific article published on 2 October 2017

Crystallization and X-ray analysis of the N-terminal core domain of a tumour-associated human DEAD-box RNA helicase, rck/p54

Crystallization and preliminary X-ray analyses of quaternary, ternary and binary protein-DNA complexes with involvement of AML1/Runx-1/CBFalpha Runt domain, CBFbeta and the C/EBPbeta bZip region

scientific article published on 25 May 2001

Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii.

scientific article published on 23 December 2010

Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis

scientific article published on 30 October 2009

Crystallization and preliminary X-ray crystallographic analysis of chitinase F1 (ChiF1) from the alkaliphilic Nocardiopsis sp. strain F96.

scientific article published on 20 October 2004

Crystallization and preliminary X-ray diffraction studies of hyperthermophilic archaeal Rieske-type ferredoxin (ARF) from Sulfolobus solfataricus P1

scientific article published on 24 June 2010

Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004

scientific article published on 21 November 2007

Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment

scientific article published on 21 July 2004

Crystallization and preliminary X-ray diffraction studies of the prototypal homologue of mitoNEET (Tth-NEET0026) from the extreme thermophile Thermus thermophilus HB8.

scientific article published on 28 November 2008

Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima

scientific article published on 19 August 2003

Crystallization and preliminary crystallographic analysis of endo-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp. strain F96.

scientific article

Crystallization and preliminary crystallographic analysis of the complex between triiodothyronine and the bb' fragment of rat protein disulfide isomerase

scientific article published on 28 March 2012

Crystals of ternary protein-DNA complexes composed of DNA-binding domains of c-Myb or v-Myb, C/EBPalpha or C/EBPbeta and tom-1A promoter fragment

scientific article published on 25 October 2001

Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines

scientific article published on 31 January 2020

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography

scientific article

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline

scientific article published on 02 October 2013

Dissection of hydrogen bond interaction network around an iron-sulfur cluster by site-specific isotope labeling of hyperthermophilic archaeal Rieske-type ferredoxin

scientific article published on 20 November 2012

Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method

scientific article published on 25 February 2021

Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.

scientific article published on 30 April 2010

Expression, crystallization and preliminary crystallographic analysis of the PAS domain of RsbP, a stress-response phosphatase from Bacillus subtilis

scientific article published on 22 May 2009

Expression, purification, crystallization and preliminary X-ray analysis of the Met244Ala variant of catalase-peroxidase (KatG) from the haloarchaeon Haloarcula marismortui

scientific article published on 24 October 2007

Glutathione ethylester, a novel protein refolding reagent, enhances both the efficiency of refolding and correct disulfide formation

scientific article published on 01 August 2012

High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine

scientific article

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments.

scientific article published on 17 August 2013

ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization

scientific article published on 7 June 2011

Improvement of alkaliphily of Bacillus alkaline xylanase by introducing amino acid substitutions both on catalytic cleft and protein surface.

scientific article published on 7 April 2009

In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase

scientific article published on 18 December 2018

In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction

scientific article

In situ crystal data-collection and ligand-screening system at SPring-8

Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays

scientific article published on 14 June 2019

Mail-in data collection at SPring-8 protein crystallography beamlines

scientific article

Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter

scientific article

Mechanism of metal activation of human hematopoietic prostaglandin D synthase

scientific article

Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal

scientific article

Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus.

scientific article

Protein encapsulation within synthetic molecular hosts

scientific article published in Nature Communications

Protein microcrystallography using synchrotron radiation

scientific article

RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation.

scientific article published in March 2006

Remote access and automation of SPring-8 MX beamlines

article

Resonance Raman characterization of archaeal and bacterial Rieske protein variants with modified hydrogen bond network around the [2Fe-2S] center.

scientific article

SPring-8 BL41XU, a high-flux macromolecular crystallography beamline.

scientific article published on 2 October 2013

Self-assembly of tetravalent Goldberg polyhedra from 144 small components

scientific article published in Nature

Short-lived intermediate in NO generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography

Structural Basis for Conformational Dynamics of GTP-bound Ras Protein

scientific article

Structural Basis for Polymer Packing and Solvation Properties of the Organogermanium Crystalline Polymer Propagermanium and Its Derivatives

scientific article published on 2 June 2015

Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL

scientific article published on July 2016

Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b

scientific article published on 5 December 2016

Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming

scientific article

Structural basis for intramolecular interaction of post-translationally modified H-Ras•GTP prepared by protein ligation

scientific article published on 20 July 2017

Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop.

scientific article published on 8 March 2004

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

scientific article published in December 2005

Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain

scientific article

Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy

scientific article published on 29 July 2017

Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+

scientific article

Structure of Thermus thermophilus homoisocitrate dehydrogenase in complex with a designed inhibitor

scientific article

Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis

scientific article

Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling

scientific article published on 15 March 2001

The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96

scientific article

The 1.48 A resolution crystal structure of the homotetrameric cytidine deaminase from mouse.

scientific article published in June 2006

The flexible C-terminal region of Aspergillus terreus blasticidin S deaminase: identification of its functional roles with deletion enzymes.

scientific article published in January 2002

Trichromatic Concept Optimizes MAD Experiments in Synchrotron X-Ray Crystallography

scientific article published on 01 September 2002

Unpaired Electron Spin Density Distribution across Reduced [2Fe-2S] Cluster Ligands by 13Cβ-Cysteine Labeling.

scientific article published on 26 December 2017

ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography

scientific article published on 28 January 2019

[Atomic structure of bovine rhodopsin, a seven transmembrane receptor: toward the elucidation of GPCR's molecular mechanism]

scientific article published on 01 May 2001

[SPring-8 structural biology beamline]

scientific article published on 01 May 2010

List of works by Takashi Kumasaka

A calcium-dependent xylan-binding domain of alkaline xylanase from alkaliphilic Bacillus sp. strain 41M-1

A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.

A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate.

A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method

Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals

Assembly of homogeneous norovirus-like particles accomplished by amino acid substitution.

Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8.

Characterization of Nocardiopsis beta-1,3-glucanase with additional carbohydrate-binding domains

Cloning and functional characterization of the copper/zinc superoxide dismutase gene from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6

Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme

Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals

Contribution of salt bridges to alkaliphily of Bacillus alkaline xylanase

Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus

Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor

Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel

Crystal structure of rhodopsin: A G protein-coupled receptor

Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor

Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis

Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii

Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants

Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics.

Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain

Crystallization and X-ray analysis of the N-terminal core domain of a tumour-associated human DEAD-box RNA helicase, rck/p54

Crystallization and preliminary X-ray analyses of quaternary, ternary and binary protein-DNA complexes with involvement of AML1/Runx-1/CBFalpha Runt domain, CBFbeta and the C/EBPbeta bZip region

Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii.

Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis

Crystallization and preliminary X-ray crystallographic analysis of chitinase F1 (ChiF1) from the alkaliphilic Nocardiopsis sp. strain F96.

Crystallization and preliminary X-ray diffraction studies of hyperthermophilic archaeal Rieske-type ferredoxin (ARF) from Sulfolobus solfataricus P1

Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004

Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment

Crystallization and preliminary X-ray diffraction studies of the prototypal homologue of mitoNEET (Tth-NEET0026) from the extreme thermophile Thermus thermophilus HB8.

Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima

Crystallization and preliminary crystallographic analysis of endo-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp. strain F96.

Crystallization and preliminary crystallographic analysis of the complex between triiodothyronine and the bb' fragment of rat protein disulfide isomerase

Crystals of ternary protein-DNA complexes composed of DNA-binding domains of c-Myb or v-Myb, C/EBPalpha or C/EBPbeta and tom-1A promoter fragment

Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline

Dissection of hydrogen bond interaction network around an iron-sulfur cluster by site-specific isotope labeling of hyperthermophilic archaeal Rieske-type ferredoxin

Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method

Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.

Expression, crystallization and preliminary crystallographic analysis of the PAS domain of RsbP, a stress-response phosphatase from Bacillus subtilis

Expression, purification, crystallization and preliminary X-ray analysis of the Met244Ala variant of catalase-peroxidase (KatG) from the haloarchaeon Haloarcula marismortui

Glutathione ethylester, a novel protein refolding reagent, enhances both the efficiency of refolding and correct disulfide formation

High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments.

ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization

Improvement of alkaliphily of Bacillus alkaline xylanase by introducing amino acid substitutions both on catalytic cleft and protein surface.

In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase

In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction

In situ crystal data-collection and ligand-screening system at SPring-8

Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays

Mail-in data collection at SPring-8 protein crystallography beamlines

Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter

Mechanism of metal activation of human hematopoietic prostaglandin D synthase

Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal

Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus.

Protein encapsulation within synthetic molecular hosts

Protein microcrystallography using synchrotron radiation

RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation.

Remote access and automation of SPring-8 MX beamlines

Resonance Raman characterization of archaeal and bacterial Rieske protein variants with modified hydrogen bond network around the [2Fe-2S] center.

SPring-8 BL41XU, a high-flux macromolecular crystallography beamline.

Self-assembly of tetravalent Goldberg polyhedra from 144 small components

Short-lived intermediate in NO generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography

Structural Basis for Conformational Dynamics of GTP-bound Ras Protein

Structural Basis for Polymer Packing and Solvation Properties of the Organogermanium Crystalline Polymer Propagermanium and Its Derivatives

Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL

Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b

Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming

Structural basis for intramolecular interaction of post-translationally modified H-Ras•GTP prepared by protein ligation

Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop.

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain