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6JY0
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BU of 6jy0 by Molmil
CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
Descriptor: Flagellin
Authors:Yamaguchi, T, Toma, S, Terahara, N, Miyata, T, Minamino, T, Ashikara, M, Namba, K, Kato, T.
Deposit date:2019-04-25
Release date:2020-02-19
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (3.56 Å)
Cite:Structural and Functional Comparison ofSalmonellaFlagellar Filaments Composed of FljB and FliC.
Biomolecules, 10, 2020
4YL4
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BU of 4yl4 by Molmil
1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin
Descriptor: COPPER (II) ION, GLYCEROL, Pseudoazurin
Authors:Yamaguchi, T, Asamura, S, Takashina, A, Unno, M, Kohzuma, T.
Deposit date:2015-03-05
Release date:2016-03-09
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling
Rsc Adv, 6, 2016
7CLR
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BU of 7clr by Molmil
CryoEM structure of S.typhimurium flagellar LP ring
Descriptor: Flagellar L-ring protein, Flagellar P-ring protein
Authors:Yamaguchi, T, Makino, F, Miyata, T, Minamino, T, Kato, T, Namba, K.
Deposit date:2020-07-21
Release date:2021-06-02
Last modified:2021-12-22
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Structure of the molecular bushing of the bacterial flagellar motor.
Nat Commun, 12, 2021
5XMO
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BU of 5xmo by Molmil
X-ray crystal structure of Pseudoazurin Met16Phe/Thr36Lys variant
Descriptor: COPPER (II) ION, Pseudoazurin
Authors:Yamaguchi, T, Kohzuma, T.
Deposit date:2017-05-16
Release date:2018-05-16
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.19 Å)
Cite:X-ray Crystallographic Analysis of M16F/T36K Double Mutant of Pseudoazurin
Photon Factory Activity Report, 34, 2017
5Y23
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BU of 5y23 by Molmil
X-ray crystal structure of Pseudoazurin Met16Phe variant
Descriptor: COPPER (II) ION, GLYCEROL, Pseudoazurin
Authors:Yamaguchi, T, Akao, K, Kohzuma, T.
Deposit date:2017-07-23
Release date:2018-07-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:X-ray crystal structure of Pseudoazurin Met16Phe variant
To Be Published
8I50
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BU of 8i50 by Molmil
Crystal structure of DNA octamer containing GuNA[Me,Me]
Descriptor: DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')
Authors:Aoyama, H, Obika, S, Yamaguchi, T.
Deposit date:2023-01-21
Release date:2023-08-09
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (0.95 Å)
Cite:Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
8HIS
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BU of 8his by Molmil
Crystal structure of DNA decamer containing GuNA[Me,tBu]
Descriptor: CACODYLIC ACID, DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3')
Authors:Aoyama, H, Obika, S, Yamaguchi, T.
Deposit date:2022-11-21
Release date:2023-08-09
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
8HU5
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BU of 8hu5 by Molmil
Crystal structure of DNA octamer containing GuNA[Me,tBu]
Descriptor: DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3')
Authors:Aoyama, H, Obika, H, Yamaguchi, T.
Deposit date:2022-12-22
Release date:2023-08-09
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (0.93 Å)
Cite:Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
5Z0X
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BU of 5z0x by Molmil
X-ray Crystal Structure of Pseudoazurin Met16Tyr Variant
Descriptor: COPPER (II) ION, GLYCEROL, Pseudoazurin
Authors:Saito, Y, Yamaguchi, T, Kohzuma, T.
Deposit date:2017-12-22
Release date:2018-12-26
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.46 Å)
Cite:X-ray Crystal Structure of Pseudoazurin Met16Tyr Variant
To Be Published
5YW3
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BU of 5yw3 by Molmil
X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant
Descriptor: CHLORIDE ION, COPPER (II) ION, Pseudoazurin
Authors:Sakai, C, Yamaguchi, T, Kohzuma, T.
Deposit date:2017-11-28
Release date:2018-11-28
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.19 Å)
Cite:X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant
To Be Published
4WDT
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BU of 4wdt by Molmil
17beta-HSD5 in complex with 2-nitro-5-(phenylsulfonyl)phenol
Descriptor: 2-nitro-5-(phenylsulfonyl)phenol, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Amano, Y, Yamaguchi, T.
Deposit date:2014-09-09
Release date:2015-04-15
Last modified:2022-12-14
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
4WDU
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BU of 4wdu by Molmil
17beta-HSD5 in complex with 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide
Descriptor: 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Amano, Y, Yamaguchi, T.
Deposit date:2014-09-09
Release date:2015-04-15
Last modified:2022-12-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
4WDX
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BU of 4wdx by Molmil
17beta-HSD5 in complex with [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone
Descriptor: Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone
Authors:Amano, Y, Yamaguchi, T.
Deposit date:2014-09-09
Release date:2015-04-15
Last modified:2022-12-14
Method:X-RAY DIFFRACTION (1.64 Å)
Cite:Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
4WDW
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BU of 4wdw by Molmil
17beta-HSD5 in complex with 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone
Descriptor: 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Amano, Y, Yamaguchi, T.
Deposit date:2014-09-09
Release date:2015-04-15
Last modified:2022-12-14
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
5WV4
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BU of 5wv4 by Molmil
X-ray Crystal Structure of Pseudoazurin Met16Gly variant
Descriptor: COPPER (II) ION, Pseudoazurin
Authors:Tamaoki, S, Yamaguchi, T, Kohzuma, T.
Deposit date:2016-12-22
Release date:2017-12-27
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:X-ray Crystal Structure of Pseudoazurin Met16Gly variant
To Be Published
2NVL
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BU of 2nvl by Molmil
Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form)
Descriptor: Probable peroxiredoxin
Authors:Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T.
Deposit date:2006-11-13
Release date:2007-11-20
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.36 Å)
Cite:Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
6KNF
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BU of 6knf by Molmil
CryoEM map and model of Nitrite Reductase at pH 6.2
Descriptor: COPPER (II) ION, Copper-containing nitrite reductase
Authors:Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T.
Deposit date:2019-08-05
Release date:2020-08-12
Last modified:2021-08-25
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213, 2021
6KNG
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BU of 6kng by Molmil
CryoEM map and model of Nitrite Reductase at pH 8.1
Descriptor: COPPER (II) ION, Copper-containing nitrite reductase
Authors:Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T.
Deposit date:2019-08-05
Release date:2020-08-12
Last modified:2021-08-25
Method:ELECTRON MICROSCOPY (2.85 Å)
Cite:2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213, 2021
5D9B
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BU of 5d9b by Molmil
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9D
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BU of 5d9d by Molmil
Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.701 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9C
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BU of 5d9c by Molmil
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
4XVD
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BU of 4xvd by Molmil
17beta-HSD5 in complex with 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol
Descriptor: 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Amano, Y, Yamaguchi, T, Niimi, T, Sakashita, H.
Deposit date:2015-01-27
Release date:2015-04-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.81 Å)
Cite:Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
6IFP
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BU of 6ifp by Molmil
X-ray Crystal Structure of Pseudoazurin Met16Ile Variant
Descriptor: COPPER (II) ION, Pseudoazurin
Authors:Sakai, C, Yamaguchi, T, Kohzuma, T.
Deposit date:2018-09-20
Release date:2019-09-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:X-ray Crystal Structure of Pseudoazurin Met16Leu Variant
To Be Published
4XVE
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BU of 4xve by Molmil
17beta-HSD5 in complex with 3-pentyl-2-[(pyridin-2-ylmethyl)sulfanyl]-7-(pyrrolidin-1-ylcarbonyl)quinazolin-4(3H)-one
Descriptor: 3-pentyl-2-[(pyridin-2-ylmethyl)sulfanyl]-7-(pyrrolidin-1-ylcarbonyl)quinazolin-4(3H)-one, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Amano, Y, Yamaguchi, T.
Deposit date:2015-01-27
Release date:2015-04-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
7BOW
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BU of 7bow by Molmil
Hydroxynitrile lyase from Parafonteria laminate
Descriptor: GLYCEROL, Hydroxynitrile lyase
Authors:Nuylert, A, Nakabayashi, M, Yamaguchi, T, Asano, Y.
Deposit date:2020-03-20
Release date:2021-03-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.42 Å)
Cite:Hydroxynitrile lyase from Parafonteria laminate
To Be Published

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