Author results

1WNI
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CRYSTAL STRUCTURE OF H2-PROTEINASE
Descriptor:Trimerelysin II, ZINC ION
Authors:Kumasaka, T., Yamamoto, M., Moriyama, H., Tanaka, N., Sato, M., Katsube, Y., Yamakawa, Y., Omori-Satoh, T., Iwanaga, S., Ueki, T.
Deposit date:2004-08-04
Release date:2004-08-17
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis
J.Biochem.(Tokyo), 119, 1996
2CZT
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LIPOCALIN-TYPE PROSTAGLANDIN D SYNTHASE
Descriptor:Prostaglandin-H2 D-isomerase
Authors:Kumasaka, T., Irikura, D., Ago, H., Aritake, K., Yamamoto, M., Inoue, T., Miyano, M., Urade, Y., Hayaishi, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-07-17
Release date:2006-10-03
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
J.Biol.Chem., 284, 2009
2CZU
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LIPOCALIN-TYPE PROSTAGLANDIN D SYNTHASE
Descriptor:Prostaglandin-H2 D-isomerase
Authors:Kumasaka, T., Irikura, D., Ago, H., Aritake, K., Yamamoto, M., Inoue, T., Miyano, M., Urade, Y., Hayaishi, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-07-17
Release date:2006-10-03
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
J.Biol.Chem., 284, 2009
1WN5
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CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) COMPLEXED WITH CACODYLIC ACID
Descriptor:Blasticidin-S deaminase, ZINC ION, CACODYLATE ION
Authors:Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.
Deposit date:2004-07-27
Release date:2005-10-25
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
1WN6
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CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) COMPLEXED WITH TETRAHEDRAL INTERMEDIATE OF BLASTICIDIN S
Descriptor:Blasticidin-S deaminase, ZINC ION, 6-(4-AMINO-4-HYDROXY-2-OXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-3-[3-AMINO-5-(N-METHYL-GUANIDINO)-PENT ANOYLAMINO]-3,6-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID, ...
Authors:Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.
Deposit date:2004-07-27
Release date:2005-10-25
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
2Z3G
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CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD)
Descriptor:Blasticidin-S deaminase, ZINC ION, TREHALOSE
Authors:Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.
Deposit date:2007-06-04
Release date:2007-10-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
2Z3H
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CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) COMPLEXED WITH DEAMINOHYDROXY BLASTICIDIN S
Descriptor:Blasticidin-S deaminase, ZINC ION, 1-(4-{[(3R)-3-AMINO-5-{[(Z)-AMINO(IMINO)METHYL](METHYL)AMINO}PENTANOYL]AMINO}-2,3,4-TRIDEOXY-D-ERYTHRO-HEX-2-ENOPYRANURONOSYL)-4-HYDROXYPYRIMIDIN-2(1H)-ONE
Authors:Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.
Deposit date:2007-06-04
Release date:2007-10-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
2Z3I
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CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) MUTANT E56Q COMPLEXED WITH SUBSTRATE
Descriptor:Blasticidin-S deaminase, BLASTICIDIN S, ZINC ION, ...
Authors:Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.
Deposit date:2007-06-04
Release date:2007-10-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
3AH7
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CRYSTAL STRUCTURE OF THE ISC-LIKE [2FE-2S] FERREDOXIN (FDXB) FROM PSEUDOMONAS PUTIDA JCM 20004
Descriptor:[2Fe-2S]ferredoxin, FE2/S2 (INORGANIC) CLUSTER, SODIUM ION, ...
Authors:Kumasaka, T., Shimizu, N., Ohmori, D., Iwasaki, T.
Deposit date:2010-04-20
Release date:2011-04-20
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004
To be Published
5B2Z
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H-RAS WT IN COMPLEX WITH GPPNHP (STATE 2*) BEFORE STRUCTURAL TRANSITION BY HUMIDITY CONTROL
Descriptor:GTPase HRas, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, CALCIUM ION, ...
Authors:Kumasaka, T., Miyano, N., Baba, S., Matsumoto, S., Kataoka, T., Shima, F.
Deposit date:2016-02-07
Release date:2016-06-01
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep, 6, 2016
5B30
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H-RAS WT IN COMPLEX WITH GPPNHP (STATE 1) AFTER STRUCTURAL TRANSITION BY HUMIDITY CONTROL
Descriptor:GTPase HRas, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, MAGNESIUM ION, ...
Authors:Kumasaka, T., Miyano, N., Baba, S., Matsumoto, S., Kataoka, T., Shima, F.
Deposit date:2016-02-08
Release date:2016-06-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep, 6, 2016
2Z3J
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CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) R90K MUTANT
Descriptor:Blasticidin-S deaminase, ZINC ION, CACODYLATE ION, ...
Authors:Teh, A.H., Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.
Deposit date:2007-06-04
Release date:2007-10-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
5B4S
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CRYSTAL STRUCTURE OF GH80 CHITOSANASE FROM MITSUARIA CHITOSANITABIDA
Descriptor:Chitosanase
Authors:Kumasaka, T., Yorinaga, Y., Yamamoto, M., Hamada, K., Kawamukai, M.
Deposit date:2016-04-19
Release date:2017-02-01
Last modified:2017-03-08
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida
FEBS Lett., 591, 2017
1VBR
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CRYSTAL STRUCTURE OF COMPLEX XYLANASE 10B FROM THERMOTOGA MARITIMA WITH XYLOBIOSE
Descriptor:endo-1,4-beta-xylanase B, XYLOPYRANOSE, BETA-D-XYLOPYRANOSE, ...
Authors:Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.
Deposit date:2004-03-02
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8
Proteins, 61, 2005
1VBU
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CRYSTAL STRUCTURE OF NATIVE XYLANASE 10B FROM THERMOTOGA MARITIMA
Descriptor:endo-1,4-beta-xylanase B, SULFATE ION, ACETIC ACID, ...
Authors:Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.
Deposit date:2004-03-02
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8
Proteins, 61, 2005
1EE8
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CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8
Descriptor:MUTM (FPG) PROTEIN, ZINC ION
Authors:Sugahara, M., Mikawa, T., Kumasaka, T., Yamamoto, M., Kato, R., Fukuyama, K., Inoue, Y., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2000-01-31
Release date:2001-01-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
EMBO J., 19, 2000
3AHU
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CRYSTAL STRUCTURE OF YMAH (HFQ) FROM BACILLUS SUBTILIS IN COMPLEX WITH AN RNA APTAMER.
Descriptor:Protein hfq, 5'-R(*AP*GP*AP*GP*AP*G)-3'
Authors:Baba, S., Someya, T., Kumasaka, T., Kawai, G., Nakamura, K.
Deposit date:2010-04-29
Release date:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.
To be Published
3HSB
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CRYSTAL STRUCTURE OF YMAH (HFQ) FROM BACILLUS SUBTILIS IN COMPLEX WITH AN RNA APTAMER
Descriptor:Protein hfq, RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3')
Authors:Baba, S., Someya, T., Kumasaka, T., Kawai, G., Nakamura, K.
Deposit date:2009-06-10
Release date:2010-06-23
Last modified:2012-10-03
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq
Nucleic Acids Res., 40, 2012
2HYK
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THE CRYSTAL STRUCTURE OF AN ENDO-BETA-1,3-GLUCANASE FROM ALKALIPHILIC NOCARDIOPSIS SP.STRAIN F96
Descriptor:Beta-1,3-glucanase, SULFATE ION, CALCIUM ION, ...
Authors:Fibriansah, G., Nakamura, S., Kumasaka, T.
Deposit date:2006-08-07
Release date:2007-10-02
Last modified:2017-10-18
Method:X-RAY DIFFRACTION (1.3 Å)
Cite: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.
Proteins, 69, 2007
1ERZ
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CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES
Descriptor:N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE
Authors:Nakai, T., Hasegawa, T., Yamashita, E., Yamamoto, M., Kumasaka, T., Ueki, T., Nanba, H., Ikenaka, Y., Takahashi, S., Sato, M., Tsukihara, T.
Deposit date:2000-04-06
Release date:2001-04-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
Structure Fold.Des., 8, 2000
1UIR
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CRYSTAL STRUCTURE OF POLYAMINE AMINOPROPYLTRANSFEASE FROM THERMUS THERMOPHILUS
Descriptor:Polyamine Aminopropyltransferase
Authors:Ganbe, T., Ohnuma, M., Sato, T., Kumasaka, T., Oshima, T., Tanaka, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-07-18
Release date:2003-08-05
Last modified:2014-01-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus
J.Mol.Biol., 408, 2011
1UJ0
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CRYSTAL STRUCTURE OF STAM2 SH3 DOMAIN IN COMPLEX WITH A UBPY-DERIVED PEPTIDE
Descriptor:signal transducing adaptor molecule (SH3 domain and ITAM motif) 2, deubiquitinating enzyme UBPY, PHOSPHATE ION
Authors:Kaneko, T., Kumasaka, T., Ganbe, T., Sato, T., Miyazawa, K., Kitamura, N., Tanaka, N.
Deposit date:2003-07-24
Release date:2003-12-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain.
J.Biol.Chem., 278, 2003
1V3T
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CRYSTAL STRUCTURE OF LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE
Descriptor:leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-11-05
Release date:2004-07-13
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
1V3U
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CRYSTAL STRUCTURE OF LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE IN APO FORM
Descriptor:leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase, CHLORIDE ION
Authors:Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-11-05
Release date:2004-07-13
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
1V3V
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CRYSTAL STRUCTURE OF LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEXED WITH NADP AND 15-OXO-PGE2
Descriptor:leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase, CHLORIDE ION, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ...
Authors:Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-11-06
Release date:2004-07-13
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004