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PDB: 51 件
7FJK
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Tyrosine phenol-lyase from pantoea agglomerans
分子名称: 1,2-ETHANEDIOL, CITRIC ACID, DI(HYDROXYETHYL)ETHER, ...
著者Katayama, T, Mikamii, B, Byun, Z.
登録日2021-08-04
公開日2022-08-10
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献Faecal microbiota-dependent phenol production from tyrosine
To Be Published
4H04
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BU of 4h04 by Molmil
Lacto-N-biosidase from Bifidobacterium bifidum
分子名称: Lacto-N-biosidase, SULFATE ION, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
著者Ito, T, Katayama, T, Wada, J, Suzuki, R, Ashida, H, Wakagi, T, Yamamoto, K, Fushinobu, S.
登録日2012-09-07
公開日2013-03-20
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
J.Biol.Chem., 288, 2013
4JAW
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Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline
分子名称: 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL, Lacto-N-biosidase, SULFATE ION, ...
著者Ito, T, Katayama, T, Stubbs, K.A, Fushinobu, S.
登録日2013-02-19
公開日2013-03-20
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
J.Biol.Chem., 288, 2013
5GQC
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Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, ligand-free form
分子名称: CALCIUM ION, Lacto-N-biosidase, SODIUM ION
著者Yamada, C, Arakawa, T, Katayama, T, Fushinobu, S.
登録日2016-08-07
公開日2017-04-19
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.36 Å)
主引用文献Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Cell Chem Biol, 24, 2017
5GQG
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Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, galacto-N-biose complex
分子名称: CALCIUM ION, Lacto-N-biosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
著者Yamada, C, Arakawa, T, Katayama, T, Fushinobu, S.
登録日2016-08-07
公開日2017-04-19
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Cell Chem Biol, 24, 2017
5GQF
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Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, lacto-N-biose complex
分子名称: CALCIUM ION, Lacto-N-biosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
著者Yamada, C, Arakawa, T, Katayama, T, Fushinobu, S.
登録日2016-08-07
公開日2017-04-19
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.82 Å)
主引用文献Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Cell Chem Biol, 24, 2017
2RU8
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DnaT C-terminal domain
分子名称: Primosomal protein 1
著者Abe, Y, Tani, J, Fujiyama, S, Urabe, M, Sato, K, Aramaki, T, Katayama, T, Ueda, T.
登録日2014-01-29
公開日2014-10-08
最終更新日2023-06-14
実験手法SOLUTION NMR
主引用文献Structure and mechanism of the primosome protein DnaT-functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex.
Febs J., 281, 2014
2RT6
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Backbone 1H, 13C, and 15N Chemical Shift Assignments for PriC N-terminal domain
分子名称: Primosomal replication protein N''
著者Aramaki, T, Abe, Y, Katayama, T, Ueda, T.
登録日2013-04-24
公開日2013-08-07
最終更新日2023-06-14
実験手法SOLUTION NMR
主引用文献Solution structure of the N-terminal domain of a replication restart primosome factor, PriC, in Escherichia coli.
Protein Sci., 22, 2013
2E0G
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DnaA N-terminal domain
分子名称: Chromosomal replication initiator protein dnaA
著者Abe, Y, Katayama, T, Ueda, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2006-10-07
公開日2007-05-01
最終更新日2023-06-14
実験手法SOLUTION NMR
主引用文献Structure and Function of DnaA N-Terminal Domains: Specific Sites and Mechanisms in Inter-DnaA Interaction and in DnaB Helicase Loading on oriC
To be Published
6KZA
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Crystal structure of the complex of the interaction domains of E. coli DnaB helicase and DnaC helicase loader
分子名称: DNA replication protein DnaC, Replicative DNA helicase
著者Nagata, K, Okada, A, Ohtsuka, J, Ohkuri, T, Akama, Y, Sakiyama, Y, Miyazaki, E, Horita, S, Katayama, T, Ueda, T, Tanokura, M.
登録日2019-09-23
公開日2019-11-20
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding.
J.Biochem., 167, 2020
4UNI
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BU of 4uni by Molmil
beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 in complex with galactose
分子名称: BETA-GALACTOSIDASE, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
著者Viborg, A.H, Fredslund, F, Katayama, T, Nielsen, S.K, Svensson, B, Kitaoka, M, Lo Leggio, L, Abou Hachem, M.
登録日2014-05-28
公開日2014-10-15
最終更新日2024-01-10
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium.
Mol. Microbiol., 2014
4UOQ
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BU of 4uoq by Molmil
Nucleophile mutant (E324A) of beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04
分子名称: BETA-GALACTOSIDASE, DI(HYDROXYETHYL)ETHER, TETRAETHYLENE GLYCOL, ...
著者Viborg, A.H, Fredslund, F, Katayama, T, Nielsen, S.K, Svensson, B, Kitaoka, M, Lo Leggio, L, Abou Hachem, M.
登録日2014-06-09
公開日2014-10-22
最終更新日2024-01-10
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium.
Mol. Microbiol., 2014
2EAB
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Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form)
分子名称: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Alpha-fucosidase, ...
著者Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R.
登録日2007-01-31
公開日2007-04-24
最終更新日2011-07-13
実験手法X-RAY DIFFRACTION (1.12 Å)
主引用文献Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
4UOZ
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BU of 4uoz by Molmil
beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 nucleophile mutant E324A in complex with galactose
分子名称: BETA-GALACTOSIDASE, TRIETHYLENE GLYCOL, ZINC ION, ...
著者Viborg, A.H, Fredslund, F, Katayama, T, Nielsen, S.K, Svensson, B, Kitaoka, M, Lo Leggio, L, Abou Hachem, M.
登録日2014-06-11
公開日2014-10-15
最終更新日2024-01-10
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium.
Mol. Microbiol., 2014
6HUR
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BU of 6hur by Molmil
2'-fucosyllactose and 3-fucosyllactose binding protein from Bifidobacterium longum infantis, bound with 2'-fucosyllactose
分子名称: 2-(2-METHOXYETHOXY)ETHANOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ABC transporter substrate-binding protein, ...
著者Ejby, M, Abou Hachem, M, Lo Leggio, L, Katayama, T, Sakanaka, M.
登録日2018-10-09
公開日2019-09-04
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (1.297 Å)
主引用文献Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis.
Sci Adv, 5, 2019
7WDT
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6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S
分子名称: 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose, Beta-N-acetylhexosaminidase, ...
著者Yamada, C, Kashima, T, Fushinobu, S, Katoh, T, Katayama, T.
登録日2021-12-22
公開日2022-12-28
最終更新日2023-06-14
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
7WDU
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6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S
分子名称: Beta-N-acetylhexosaminidase, CALCIUM ION, [[(3R,4R,5S,6R)-3-acetamido-4,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-2-ylidene]amino] N-phenylcarbamate
著者Kashima, T, Yamada, C, Fushinobu, S, Katoh, T, Katayama, T.
登録日2021-12-22
公開日2022-12-28
最終更新日2023-06-14
実験手法X-RAY DIFFRACTION (2.23 Å)
主引用文献A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
2EAE
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Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products
分子名称: Alpha-fucosidase, CALCIUM ION, alpha-L-fucopyranose, ...
著者Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R.
登録日2007-01-31
公開日2007-04-24
最終更新日2021-11-10
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
2EAC
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Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin
分子名称: (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL, Alpha-fucosidase, CALCIUM ION
著者Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R.
登録日2007-01-31
公開日2007-04-24
最終更新日2011-07-13
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
1WOC
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Crystal structure of PriB
分子名称: Primosomal replication protein n
著者Shioi, S, Ose, T, Maenaka, K, Abe, Y, Kohda, D, Katayama, T, Ueda, T.
登録日2004-08-13
公開日2005-01-25
最終更新日2012-12-05
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site
Biochem.Biophys.Res.Commun., 326, 2005
5XB7
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BU of 5xb7 by Molmil
GH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis subsp. lactis Bl-04
分子名称: Beta-galactosidase, GLYCEROL, SULFATE ION
著者Viborg, A.H, Katayama, T, Arakawa, T, Abou Hachem, M, Lo Leggio, L, Kitaoka, M, Svensson, B, Fushinobu, S.
登録日2017-03-16
公開日2017-11-01
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Discovery of alpha-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.
J. Biol. Chem., 292, 2017
1C7G
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TYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA
分子名称: PYRIDOXAL-5'-PHOSPHATE, TYROSINE PHENOL-LYASE
著者Mikami, B, Yamamoto, Y, Katayama, T, Suzuki, H.
登録日2000-02-18
公開日2003-12-09
最終更新日2023-08-09
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献The Structure of Tyrosine Phenol-Lyase from Erwinia Herbicola
To be Published
5YCQ
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Unique Specificity-Enhancing Factor for the AAA+ Lon Protease
分子名称: Heat shock protein HspQ
著者Abe, Y, Shioi, S, Kita, S, Nakata, H, Maenaka, K, Kohda, D, Katayama, T, Ueda, T.
登録日2017-09-08
公開日2018-04-11
実験手法X-RAY DIFFRACTION (2.503 Å)
主引用文献X-ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation
FEBS Lett., 591, 2017
1J1V
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BU of 1j1v by Molmil
Crystal structure of DnaA domainIV complexed with DnaAbox DNA
分子名称: 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3', 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3', Chromosomal replication initiator protein dnaA
著者Fujikawa, N, Kurumizaka, H, Nureki, O, Terada, T, Shirouzu, M, Katayama, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2002-12-18
公開日2003-04-22
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structural basis of replication origin recognition by the DnaA protein
NUCLEIC ACIDS RES., 31, 2003
7VFR
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GltA N83K mutant from Bifidobacterium infantis JCM 1222 complexed with lacto-N-tetraose
分子名称: Extracellular solute-binding protein, family 1, SULFATE ION, ...
著者Sato, M, Sakanaka, M, Katayama, T, Fushinobu, S.
登録日2021-09-13
公開日2022-09-14
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.56 Å)
主引用文献Short stretch sequence of a milk oligosaccharide transporter represents the phenotypic selection trajectory in infant gut microbiome
To Be Published

 

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