4WHM
 
 | | Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with UDP | | Descriptor: | ACETATE ION, GLYCEROL, UDP-glucose:anthocyanidin 3-O-glucosyltransferase, ... | | Authors: | Hiromoto, T, Honjo, E, Tamada, T, Kuroki, R. | | Deposit date: | 2014-09-23 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.851 Å) | | Cite: | Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
Protein Sci., 24, 2015
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8W6X
 | | Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CHLORIDE ION, FE3-S4 CLUSTER, ... | | Authors: | Hiromoto, T, Tamada, T. | | Deposit date: | 2023-08-30 | | Release date: | 2023-09-13 | | Last modified: | 2023-11-15 | | Method: | NEUTRON DIFFRACTION (1.04 Å), X-RAY DIFFRACTION | | Cite: | New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase.
Chem Sci, 14, 2023
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3H65
 | | The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin | | Descriptor: | (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL, 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine, 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN, ... | | Authors: | Hiromoto, T, Warkentin, E, Shima, S, Ermler, U. | | Deposit date: | 2009-04-23 | | Release date: | 2009-09-01 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | The crystal structure of an [Fe]-hydrogenase-substrate complex reveals the framework for H2 activation.
Angew.Chem.Int.Ed.Engl., 48, 2009
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4REN
 | | Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with petunidin | | Descriptor: | 2-(3,4-dihydroxy-5-methoxyphenyl)-3,5,7-trihydroxychromenium, GLYCEROL, UDP-glucose:anthocyanidin 3-O-glucosyltransferase | | Authors: | Hiromoto, T, Honjo, E, Tamada, T, Kuroki, R. | | Deposit date: | 2014-09-23 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.704 Å) | | Cite: | Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
Protein Sci., 24, 2015
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4REM
 | | Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with delphinidin | | Descriptor: | 3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)chromenium, GLYCEROL, UDP-glucose:anthocyanidin 3-O-glucosyltransferase | | Authors: | Hiromoto, T, Honjo, E, Tamada, T, Kuroki, R. | | Deposit date: | 2014-09-23 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
Protein Sci., 24, 2015
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4REL
 | | Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with kaempferol | | Descriptor: | 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE, ACETATE ION, GLYCEROL, ... | | Authors: | Hiromoto, T, Honjo, E, Tamada, T, Kuroki, R. | | Deposit date: | 2014-09-23 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.754 Å) | | Cite: | Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
Protein Sci., 24, 2015
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3F46
 | | The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii | | Descriptor: | (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL, 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine, 5,10-methenyltetrahydromethanopterin hydrogenase, ... | | Authors: | Hiromoto, T, Vogt, S, Warkentin, E, Thauer, R.K, Shima, S, Ermler, U. | | Deposit date: | 2008-10-31 | | Release date: | 2009-02-10 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex.
Febs Lett., 583, 2009
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3F47
 | | The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii | | Descriptor: | 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine, 5,10-methenyltetrahydromethanopterin hydrogenase, CARBON MONOXIDE, ... | | Authors: | Hiromoto, T, Pilak, O, Warkentin, E, Thauer, R.K, Shima, S, Ermler, U. | | Deposit date: | 2008-10-31 | | Release date: | 2009-02-10 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex.
Febs Lett., 583, 2009
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2DKH
 | | Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate | | Descriptor: | 3-HYDROXYBENZOIC ACID, 3-hydroxybenzoate hydroxylase, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Hiromoto, T, Fujiwara, S, Hosokawa, K, Yamaguchi, H. | | Deposit date: | 2006-04-11 | | Release date: | 2006-10-24 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site
J.Mol.Biol., 364, 2006
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2DKI
 | | Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, under pressure of xenon gas (12 atm) | | Descriptor: | 3-HYDROXYBENZOATE HYDROXYLASE, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION, ... | | Authors: | Hiromoto, T, Fujiwara, S, Hosokawa, K, Yamaguchi, H. | | Deposit date: | 2006-04-11 | | Release date: | 2006-10-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site
J.Mol.Biol., 364, 2006
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3WC4
 | | Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea | | Descriptor: | ACETATE ION, GLYCEROL, UDP-glucose:anthocyanidin 3-O-glucosyltransferase | | Authors: | Hiromoto, T, Honjo, E, Tamada, T, Kuroki, R. | | Deposit date: | 2013-05-24 | | Release date: | 2013-10-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structure of UDP-glucose:anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
J.SYNCHROTRON RADIAT., 20, 2013
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5XPF
 | | High-resolution X-ray structure of the T26H mutant of T4 lysozyme | | Descriptor: | CHLORIDE ION, Endolysin, GLYCEROL, ... | | Authors: | Hiromoto, T, Kuroki, R. | | Deposit date: | 2017-06-01 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type.
Protein Sci., 26, 2017
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5XPE
 | | Neutron structure of the T26H mutant of T4 lysozyme | | Descriptor: | CHLORIDE ION, Endolysin, SODIUM ION | | Authors: | Hiromoto, T, Kuroki, R. | | Deposit date: | 2017-06-01 | | Release date: | 2017-10-04 | | Last modified: | 2024-04-03 | | Method: | NEUTRON DIFFRACTION (1.648 Å), X-RAY DIFFRACTION | | Cite: | Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type.
Protein Sci., 26, 2017
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4DBG
 | | Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative | | Descriptor: | RING finger protein 31, RanBP-type and C3HC4-type zinc finger-containing protein 1 | | Authors: | Yagi, H, Hiromoto, T, Mizushima, T, Kurimoto, E, Kato, K. | | Deposit date: | 2012-01-15 | | Release date: | 2012-04-04 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.71 Å) | | Cite: | A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex
Embo Rep., 13, 2012
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3AUL
 | | Crystal structure of wild-type Lys48-linked diubiquitin in an open conformation | | Descriptor: | Polyubiquitin-C | | Authors: | Hirano, T, Olivier, S, Yagi, M, Takemoto, E, Hiromoto, T, Satoh, T, Mizushima, T, Kato, K. | | Deposit date: | 2011-02-09 | | Release date: | 2011-09-07 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Conformational dynamics of wild-type Lys48-linked diubiquitin in solution
J.Biol.Chem., 286, 2011
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7XE7
 | | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH10 | | Descriptor: | Endolysin, GLYCEROL, HEXANE-1,6-DIOL | | Authors: | Tamada, T, Hiromoto, T. | | Deposit date: | 2022-03-30 | | Release date: | 2023-03-22 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.05 Å) | | Cite: | Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions.
Front Mol Biosci, 9, 2022
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7XE6
 | | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7 | | Descriptor: | Endolysin, GLYCEROL, HEXANE-1,6-DIOL, ... | | Authors: | Tamada, T, Hiromoto, T. | | Deposit date: | 2022-03-30 | | Release date: | 2023-03-22 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions.
Front Mol Biosci, 9, 2022
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7XEA
 | | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking | | Descriptor: | CHLORIDE ION, Endolysin, GLYCEROL, ... | | Authors: | Tamada, T, Hiromoto, T. | | Deposit date: | 2022-03-30 | | Release date: | 2023-03-22 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions.
Front Mol Biosci, 9, 2022
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7XE9
 | | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 20% | | Descriptor: | CHLORIDE ION, DIMETHYL SULFOXIDE, Endolysin, ... | | Authors: | Tamada, T, Hiromoto, T. | | Deposit date: | 2022-03-30 | | Release date: | 2023-03-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions.
Front Mol Biosci, 9, 2022
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7XE5
 | | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH4 | | Descriptor: | Endolysin, GLYCEROL, HEXANE-1,6-DIOL, ... | | Authors: | Tamada, T, Hiromoto, T. | | Deposit date: | 2022-03-30 | | Release date: | 2023-03-22 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions.
Front Mol Biosci, 9, 2022
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3VR0
 | | Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator | | Descriptor: | GOLD ION, Putative uncharacterized protein | | Authors: | Kumoi, K, Satoh, T, Hiromoto, T, Mizushima, T, Kamiya, Y, Noda, M, Uchiyama, S, Murata, K, Yagi, H, Kato, K. | | Deposit date: | 2012-04-02 | | Release date: | 2013-04-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | An archaeal homolog of proteasome assembly factor functions as a proteasome activator
Plos One, 8, 2013
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3WHJ
 | | Crystal structure of Nas2 N-terminal domain | | Descriptor: | CADMIUM ION, Probable 26S proteasome regulatory subunit p27, SULFATE ION | | Authors: | Satoh, T, Saeki, Y, Hiromoto, T, Wang, Y.-H, Uekusa, Y, Yagi, H, Yoshihara, H, Yagi-Utsumi, M, Mizushima, T, Tanaka, K, Kato, K. | | Deposit date: | 2013-08-26 | | Release date: | 2014-03-26 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WHK
 | | Crystal structure of PAN-Rpt5C chimera | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | | Authors: | Satoh, T, Saeki, Y, Hiromoto, T, Wang, Y.-H, Uekusa, Y, Yagi, H, Yoshihara, H, Yagi-Utsumi, M, Mizushima, T, Tanaka, K, Kato, K. | | Deposit date: | 2013-08-26 | | Release date: | 2014-03-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WHL
 | | Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Probable 26S proteasome regulatory subunit p27, Proteasome-activating nucleotidase, ... | | Authors: | Satoh, T, Saeki, Y, Hiromoto, T, Wang, Y.-H, Uekusa, Y, Yagi, H, Yoshihara, H, Yagi-Utsumi, M, Mizushima, T, Tanaka, K, Kato, K. | | Deposit date: | 2013-08-26 | | Release date: | 2014-03-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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5Y4N
 | | Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... | | Authors: | Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y. | | Deposit date: | 2017-08-04 | | Release date: | 2018-08-08 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
J.Inorg.Biochem., 177, 2017
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