1X10
 
 | | Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192A) from a Hyperthermophile, Pyrococcus furiosus | | Descriptor: | Pyrrolidone-carboxylate peptidase | | Authors: | Kaushik, J.K, Yamagata, Y, Ogasahara, K, Yutani, K. | | Deposit date: | 2005-03-31 | | Release date: | 2006-06-13 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Completely buried, non-ion-paired glutamic acid contributes favorably to the conformational stability of pyrrolidone carboxyl peptidases from hyperthermophiles.
Biochemistry, 45, 2006
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6QIQ
 | | Crystal structure of seleno-derivative CAG repeats with synthetic CMBL3a compound | | Descriptor: | CMBL3a, RNA (5'-R(*GP*CP*AP*G)-D(P*(CSL))-R(P*AP*GP*C)-3') | | Authors: | Kiliszek, A, Blaszczyk, L, Rypniewski, W, Micura, R, Nakatani, K. | | Deposit date: | 2019-01-21 | | Release date: | 2019-09-25 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.519 Å) | | Cite: | Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
Nucleic Acids Res., 47, 2019
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6QIT
 | | Crystal structure of CAG repeats with synthetic CMBL3b compound | | Descriptor: | CMBL3a, RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3') | | Authors: | Kiliszek, A, Blaszczyk, L, Rypniewski, W, Nakatani, K. | | Deposit date: | 2019-01-21 | | Release date: | 2019-09-25 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (1.501 Å) | | Cite: | Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
Nucleic Acids Res., 47, 2019
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6QIV
 | | Crystal structure of seleno-derivative CAG repeats with synthetic CMBL4 compound | | Descriptor: | CMBL4, RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3') | | Authors: | Kiliszek, A, Blaszczyk, L, Rypniewski, W, Nakatani, K. | | Deposit date: | 2019-01-21 | | Release date: | 2019-09-25 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.28 Å) | | Cite: | Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
Nucleic Acids Res., 47, 2019
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2HEB
 | | CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY | | Descriptor: | LYSOZYME, SODIUM ION | | Authors: | Takano, K, Funahashi, J, Yamagata, Y, Fujii, S, Yutani, K. | | Deposit date: | 1997-09-16 | | Release date: | 1998-01-28 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Contribution of water molecules in the interior of a protein to the conformational stability.
J.Mol.Biol., 274, 1997
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4KEP
 | | Crystal structure of 4-pyridoxolactonase, wild-type | | Descriptor: | 1,2-ETHANEDIOL, 4-pyridoxolactonase, ACETATE ION, ... | | Authors: | Kobayashi, J, Yoshikane, Y, Baba, S, Mizutani, K, Takahashi, N, Mikami, B, Yagi, T. | | Deposit date: | 2013-04-26 | | Release date: | 2014-04-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | Structure of 4-pyridoxolactonase from Mesorhizobium loti.
Acta Crystallogr.,Sect.F, 70, 2014
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4KEQ
 | | Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound | | Descriptor: | 1,2-ETHANEDIOL, 4-pyridoxolactonase, 7-hydroxy-6-methylfuro[3,4-c]pyridin-3(1H)-one, ... | | Authors: | Kobayashi, J, Yoshikane, Y, Baba, S, Mizutani, K, Takahashi, N, Mikami, B, Yagi, T. | | Deposit date: | 2013-04-26 | | Release date: | 2014-04-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.279 Å) | | Cite: | Structure of 4-pyridoxolactonase from Mesorhizobium loti.
Acta Crystallogr.,Sect.F, 70, 2014
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4JY3
 | | Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form | | Descriptor: | 1,2-ETHANEDIOL, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid, ... | | Authors: | Kobayashi, J, Yoshida, H, Kamitori, S, Hayashi, H, Mizutani, K, Takahashi, N, Mikami, B, Yagi, T. | | Deposit date: | 2013-03-29 | | Release date: | 2014-04-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
To be Published
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2HED
 | | CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY | | Descriptor: | LYSOZYME, SODIUM ION | | Authors: | Takano, K, Funahashi, J, Yamagata, Y, Fujii, S, Yutani, K. | | Deposit date: | 1997-09-16 | | Release date: | 1998-01-14 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of water molecules in the interior of a protein to the conformational stability.
J.Mol.Biol., 274, 1997
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2HEC
 | | CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY | | Descriptor: | LYSOZYME, SODIUM ION | | Authors: | Takano, K, Funahashi, J, Yamagata, Y, Fujii, S, Yutani, K. | | Deposit date: | 1997-09-16 | | Release date: | 1998-01-14 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of water molecules in the interior of a protein to the conformational stability.
J.Mol.Biol., 274, 1997
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4JY2
 | | Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, native and unliganded form | | Descriptor: | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, BETA-MERCAPTOETHANOL, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Kobayashi, J, Yoshida, H, Kamitori, S, Hayashi, H, Mizutani, K, Takahashi, N, Mikami, B, Yagi, T. | | Deposit date: | 2013-03-28 | | Release date: | 2014-04-02 | | Method: | X-RAY DIFFRACTION (1.935 Å) | | Cite: | Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
To be Published
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2HEE
 | | CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY | | Descriptor: | LYSOZYME, SODIUM ION | | Authors: | Takano, K, Funahashi, J, Yamagata, Y, Fujii, S, Yutani, K. | | Deposit date: | 1997-09-16 | | Release date: | 1998-01-14 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of water molecules in the interior of a protein to the conformational stability.
J.Mol.Biol., 274, 1997
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2HEA
 | | CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY | | Descriptor: | LYSOZYME, SODIUM ION | | Authors: | Takano, K, Funahashi, J, Yamagata, Y, Fujii, S, Yutani, K. | | Deposit date: | 1997-09-16 | | Release date: | 1998-01-14 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of water molecules in the interior of a protein to the conformational stability.
J.Mol.Biol., 274, 1997
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2HEF
 | | CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY | | Descriptor: | LYSOZYME, SODIUM ION | | Authors: | Takano, K, Funahashi, J, Yamagata, Y, Fujii, S, Yutani, K. | | Deposit date: | 1997-09-16 | | Release date: | 1998-01-14 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of water molecules in the interior of a protein to the conformational stability.
J.Mol.Biol., 274, 1997
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6KJL
 | | Xylanase J from Bacillus sp. strain 41M-1 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CALCIUM ION, ... | | Authors: | Manami, S, Teisuke, T, Nakatani, K, Katano, K, Kojima, K, Saka, N, Mikami, B, Yatsunami, R, Nakamura, S, Yasukawa, K. | | Deposit date: | 2019-07-22 | | Release date: | 2019-09-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis.
Enzyme.Microb.Technol., 130, 2019
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2AEN
 | | Crystal structure of the rotavirus strain DS-1 VP8* core | | Descriptor: | ETHANOL, GLYCEROL, Outer capsid protein VP4, ... | | Authors: | Monnier, N, Higo-Moriguchi, K, Sun, Z.-Y.J, Prasad, B.V.V, Taniguchi, K, Dormitzer, P.R. | | Deposit date: | 2005-07-22 | | Release date: | 2006-02-07 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.604 Å) | | Cite: | High-resolution molecular and antigen structure of the VP8*
core of a sialic acid-independent human rotavirus strain
J.Virol., 80, 2006
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4Y65
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4Y6I
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5ZFS
 | | Crystal structure of Arthrobacter globiformis M30 sugar epimerase which can produce D-allulose from D-fructose | | Descriptor: | ACETATE ION, D-allulose-3-epimerase, MANGANESE (II) ION | | Authors: | Yoshida, H, Yoshihara, A, Gullapalli, P.K, Ohtani, K, Akimitsu, K, Izumori, K, Kamitori, S. | | Deposit date: | 2018-03-07 | | Release date: | 2018-10-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of D-allulose from D-fructose.
Acta Crystallogr F Struct Biol Commun, 74, 2018
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7YVW
 | | NMR determination of the 2:1 binding motif structure involving cytosine flipping out for the recognition of the CGG/CGG triad DNA | | Descriptor: | 3-[3-[(7-methyl-1,8-naphthyridin-2-yl)carbamoyloxy]propylamino]propyl ~{N}-(7-methyl-1,8-naphthyridin-2-yl)carbamate, DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3') | | Authors: | Furuita, K, Yamada, T, Sakurabayashi, S, Nomura, M, Kojima, C, Nakatani, K. | | Deposit date: | 2022-08-19 | | Release date: | 2023-06-14 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA.
Nucleic Acids Res., 50, 2022
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6L9C
 | | Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 | | Descriptor: | COPPER (II) ION, Phenylethylamine oxidase, SODIUM ION | | Authors: | Murakawa, T, Kurihara, K, Shoji, M, Shibazaki, C, Sunami, T, Tamada, T, Yano, N, Yamada, T, Kusaka, K, Suzuki, M, Shigeta, Y, Kuroki, R, Hayashi, H, Yano, Y, Tanizawa, K, Adachi, M, Okajima, T. | | Deposit date: | 2019-11-08 | | Release date: | 2020-04-29 | | Last modified: | 2023-11-22 | | Method: | NEUTRON DIFFRACTION (1.14 Å), X-RAY DIFFRACTION | | Cite: | Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.
Proc.Natl.Acad.Sci.USA, 117, 2020
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7DQE
 | | Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, SULFATE ION, ... | | Authors: | Maruyama, S, Nakamoto, K, Suzuki, K, Mizutani, K, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Murata, T. | | Deposit date: | 2020-12-23 | | Release date: | 2021-12-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.694 Å) | | Cite: | The Combination of High-Speed AFM and X-ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-ATPase
To Be Published
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1WDW
 | | Structural basis of mutual activation of the tryptophan synthase a2b2 complex from a hyperthermophile, Pyrococcus furiosus | | Descriptor: | PYRIDOXAL-5'-PHOSPHATE, Tryptophan synthase alpha chain, Tryptophan synthase beta chain 1 | | Authors: | Lee, S.J, Ogasahara, K, Ma, J, Nishio, K, Ishida, M, Yamagata, Y, Tsukihara, T, Yutani, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-05-19 | | Release date: | 2005-07-12 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Conformational Changes in the Tryptophan Synthase from a Hyperthermophile upon alpha(2)beta(2) Complex Formation: Crystal Structure of the Complex
Biochemistry, 44, 2005
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6KKA
 | | Xylanase J mutant from Bacillus sp. 41M-1 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CALCIUM ION, ... | | Authors: | Suzuki, M, Takita, T, Nakatani, K. | | Deposit date: | 2019-07-24 | | Release date: | 2019-09-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.36 Å) | | Cite: | Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis.
Enzyme.Microb.Technol., 130, 2019
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7DQD
 | | Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase | | Descriptor: | GLYCEROL, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | | Authors: | Maruyama, S, Suzuki, K, Mizutani, K, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Murata, T. | | Deposit date: | 2020-12-23 | | Release date: | 2021-12-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.383 Å) | | Cite: | The combination of high-speed AFM and X-ray crystallography reveals rotary catalysis
To Be Published
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