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1A7V
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BU of 1a7v by Molmil
CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS
Descriptor: CYTOCHROME C', PROTOPORPHYRIN IX CONTAINING FE
Authors:Shibata, N, Iba, S, Misaki, S, Meyer, T.E, Bartsch, R.G, Cusanovich, M.A, Higuchi, Y, Yasuoka, N.
Deposit date:1998-03-18
Release date:1998-06-17
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure.
J.Mol.Biol., 284, 1998
1DIO
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BU of 1dio by Molmil
DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
Descriptor: COBALAMIN, POTASSIUM ION, PROTEIN (DIOL DEHYDRATASE), ...
Authors:Shibata, N, Masuda, J, Tobimatsu, T, Toraya, T, Suto, K, Morimoto, Y, Yasuoka, N.
Deposit date:1999-01-27
Release date:2000-01-30
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Structure Fold.Des., 7, 1999
1IWB
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BU of 1iwb by Molmil
Crystal structure of diol dehydratase
Descriptor: COBALAMIN, DIOL DEHYDRATASE alpha chain, DIOL DEHYDRATASE beta chain, ...
Authors:Shibata, N, Masuda, J, Morimoto, Y, Yasuoka, N, Toraya, T.
Deposit date:2002-05-01
Release date:2003-05-01
Last modified:2023-05-31
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase
Biochemistry, 41, 2002
1IUZ
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BU of 1iuz by Molmil
PLASTOCYANIN
Descriptor: COPPER (II) ION, PLASTOCYANIN, SULFATE ION
Authors:Shibata, N.
Deposit date:1996-10-06
Release date:1997-08-20
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.
J.Biol.Chem., 274, 1999
7XRN
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BU of 7xrn by Molmil
Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presence of substrate
Descriptor: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, COBALAMIN, ...
Authors:Shibata, N, Toraya, T.
Deposit date:2022-05-10
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
7XRL
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BU of 7xrl by Molmil
Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol
Descriptor: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, CALCIUM ION, ...
Authors:Shibata, N, Toraya, T.
Deposit date:2022-05-10
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
7XRM
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BU of 7xrm by Molmil
Ethanolamine ammonia-lyase complexed with AdoMeCbl
Descriptor: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, COBALAMIN, ...
Authors:Shibata, N, Toraya, T.
Deposit date:2022-05-10
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
7XRK
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BU of 7xrk by Molmil
Diol dehydratase complexed with AdoMeCbl
Descriptor: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, CALCIUM ION, COBALAMIN, ...
Authors:Shibata, N, Toraya, T.
Deposit date:2022-05-10
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
2D0P
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BU of 2d0p by Molmil
Structure of diol dehydratase-reactivating factor in nucleotide free form
Descriptor: CALCIUM ION, SULFATE ION, diol dehydratase-reactivating factor large subunit, ...
Authors:Shibata, N, Mori, K, Hieda, N, Higuchi, Y, Yamanishi, M, Toraya, T.
Deposit date:2005-08-05
Release date:2006-02-28
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Structure, 13, 2005
2D0O
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BU of 2d0o by Molmil
Structure of diol dehydratase-reactivating factor complexed with ADP and Mg2+
Descriptor: ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, SULFATE ION, ...
Authors:Shibata, N, Mori, K, Hieda, N, Higuchi, Y, Yamanishi, M, Toraya, T.
Deposit date:2005-08-05
Release date:2006-02-28
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Structure, 13, 2005
1UC5
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BU of 1uc5 by Molmil
Structure of diol dehydratase complexed with (R)-1,2-propanediol
Descriptor: AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ...
Authors:Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T.
Deposit date:2003-04-08
Release date:2003-07-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.Biol.Chem., 278, 2003
1UC4
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BU of 1uc4 by Molmil
Structure of diol dehydratase complexed with (S)-1,2-propanediol
Descriptor: AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ...
Authors:Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T.
Deposit date:2003-04-08
Release date:2003-07-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.BIOL.CHEM., 278, 2003
3ABQ
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BU of 3abq by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and 2-amino-1-propanol
Descriptor: (2S)-2-aminopropan-1-ol, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ...
Authors:Shibata, N.
Deposit date:2009-12-21
Release date:2010-06-02
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
3ABR
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BU of 3abr by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)
Descriptor: COBALAMIN, Ethanolamine ammonia-lyase heavy chain, Ethanolamine ammonia-lyase light chain, ...
Authors:Shibata, N.
Deposit date:2009-12-21
Release date:2010-06-02
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
3ABO
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BU of 3abo by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and ethanolamine
Descriptor: COBALAMIN, ETHANOLAMINE, Ethanolamine ammonia-lyase heavy chain, ...
Authors:Shibata, N.
Deposit date:2009-12-21
Release date:2010-06-02
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
3ABS
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BU of 3abs by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with adeninylpentylcobalamin and ethanolamine
Descriptor: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, ETHANOLAMINE, Ethanolamine ammonia-lyase heavy chain, ...
Authors:Shibata, N.
Deposit date:2009-12-21
Release date:2010-06-02
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
2D5G
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BU of 2d5g by Molmil
Structure of ubiquitin fold protein R767E mutant
Descriptor: Axin-1, MERCURY (II) ION
Authors:Shibata, N, Higuchi, Y.
Deposit date:2005-11-01
Release date:2006-11-01
Last modified:2021-11-10
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structure of ubiquitin fold protein R767E mutant
to be published
2E83
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BU of 2e83 by Molmil
T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Descriptor: FLAVIN MONONUCLEOTIDE, FMN-binding protein
Authors:Shibata, N, Higuchi, Y.
Deposit date:2007-01-17
Release date:2008-01-15
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Structure of T31V mutant of FMN-binding protein from Desulfovibrio vulgaris Miyazaki F
To be Published
5YSR
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BU of 5ysr by Molmil
Ethanolamine ammonia-lyase, AdoCbl/2-amino-1-propanol
Descriptor: 5'-DEOXYADENOSINE, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ...
Authors:Shibata, N.
Deposit date:2017-11-14
Release date:2018-09-19
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
5YRV
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BU of 5yrv by Molmil
Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal
Descriptor: 5'-DEOXYADENOSINE, CALCIUM ION, CHLORIDE ION, ...
Authors:Shibata, N.
Deposit date:2017-11-10
Release date:2018-09-19
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
5YRT
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BU of 5yrt by Molmil
Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal
Descriptor: 5'-DEOXYADENOSINE, CALCIUM ION, CHLORIDE ION, ...
Authors:Shibata, N.
Deposit date:2017-11-10
Release date:2018-09-19
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
5YSN
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BU of 5ysn by Molmil
Ethanolamine ammonia-lyase, AdoCbl/substrate-free
Descriptor: 5'-DEOXYADENOSINE, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ...
Authors:Shibata, N.
Deposit date:2017-11-14
Release date:2018-09-19
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.001 Å)
Cite:Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
5YSH
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BU of 5ysh by Molmil
Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal
Descriptor: 5'-DEOXYADENOSINE, CALCIUM ION, COBALAMIN, ...
Authors:Shibata, N.
Deposit date:2017-11-14
Release date:2018-09-19
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
1WSP
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BU of 1wsp by Molmil
Crystal structure of axin dix domain
Descriptor: Axin 1 protein, BENZOIC ACID, MERCURY (II) ION
Authors:Shibata, N, Hanamura, T, Yamamoto, R, Ueda, Y, Yamamoto, H, Kikuchi, A, Higuchi, Y.
Deposit date:2004-11-08
Release date:2006-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Crystal structure of axin dix domain
to be published
3ANY
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BU of 3any by Molmil
Crystal structure of ethanolamine ammonia-lyase from escherichia coli complexed with CN-CBL and (R)-2-amino-1-propanol
Descriptor: (2R)-2-aminopropan-1-ol, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ...
Authors:Shibata, N.
Deposit date:2010-09-16
Release date:2011-08-03
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:How coenzyme B12-dependent ethanolamine ammonia-lyase deals with both enantiomers of 2-amino-1-propanol as substrates: structure-based rationalization.
Biochemistry, 50, 2011

217705

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