7C86
 
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2020-05-28 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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7EIH
 | | Ancestral L-Lys oxidase (ligand free form) | | Descriptor: | FAD dependent enzyme, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION | | Authors: | Sugiura, S, Nakano, S, Niwa, M, Hasebe, F, Ito, S. | | Deposit date: | 2021-03-31 | | Release date: | 2021-08-11 | | Last modified: | 2022-02-23 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining.
J.Biol.Chem., 297, 2021
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7EII
 | | Ancestral L-Lys oxidase K387A variant (L-Lys binding form) | | Descriptor: | FAD dependent L-Lys oxidase, FLAVIN-ADENINE DINUCLEOTIDE, LYSINE | | Authors: | Sugiura, S, Nakano, S, Niwa, M, Hasebe, F, Ito, S. | | Deposit date: | 2021-03-31 | | Release date: | 2021-08-11 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining.
J.Biol.Chem., 297, 2021
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7EIJ
 | | Ancestral L-Lys oxidase K387A variant (L-Arg binding form) | | Descriptor: | ARGININE, FAD dependent L-Lys oxidase, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Sugiura, S, Nakano, S, Niwa, M, Hasebe, F, Ito, S. | | Deposit date: | 2021-03-31 | | Release date: | 2021-08-11 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining.
J.Biol.Chem., 297, 2021
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7CFO
 | | Crystal structure of human RXRalpha ligand binding domain complexed with CBTF-EE. | | Descriptor: | 1-[3-(2-ethoxyethoxy)-5,5,8,8-tetramethyl-6,7-dihydronaphthalen-2-yl]-2-(trifluoromethyl)benzimidazole-5-carboxylic acid, GLYCEROL, Retinoic acid receptor RXR-alpha | | Authors: | Watanabe, M, Fujihara, M, Motoyama, T, Kawasaki, M, Yamada, S, Takamura, Y, Ito, S, Makishima, M, Nakano, S, Kakuta, H. | | Deposit date: | 2020-06-27 | | Release date: | 2021-01-06 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Discovery of a "Gatekeeper" Antagonist that Blocks Entry Pathway to Retinoid X Receptors (RXRs) without Allosteric Ligand Inhibition in Permissive RXR Heterodimers.
J.Med.Chem., 64, 2021
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7DQB
 | | Crystal structure of an IclR homolog complexed with 4-hydroxybenzoate from Microbacterium hydrocarbonoxydans in P212121 form | | Descriptor: | IclR homolog, P-HYDROXYBENZOIC ACID | | Authors: | Akiyama, T, Sasaki, Y, Ito, S, Yajima, S. | | Deposit date: | 2020-12-23 | | Release date: | 2021-05-05 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.101 Å) | | Cite: | Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding.
Biochim Biophys Acta Proteins Proteom, 1869, 2021
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7D5M
 | | Crystal structure of inositol dehydrogenase homolog complexed with NAD+ from Azotobacter vinelandii | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, Oxidoreductase | | Authors: | Fukano, K, Ono, T, Suzuki, M, Takenoya, M, Ito, S, Sasaki, Y, Yajima, S. | | Deposit date: | 2020-09-27 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal structure of inositol dehydrogenase complexed with NAD+ from Azotobacter vinelandii
To Be Published
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7D5N
 | | Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii | | Descriptor: | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Oxidoreductase | | Authors: | Fukano, K, Ono, T, Suzuki, M, Takenoya, M, Ito, S, Sasaki, Y, Yajima, S. | | Deposit date: | 2020-09-27 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of inositol dehydrogenase complexed with NADH and myo-inositol from Azotobacter vinelandii
To Be Published
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2ZE0
 | | Alpha-glucosidase GSJ | | Descriptor: | Alpha-glucosidase, CALCIUM ION | | Authors: | Shirai, T, Hung, V.S, Morinaka, K, Kobayashi, T, Ito, S. | | Deposit date: | 2007-12-04 | | Release date: | 2007-12-18 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria
Proteins, 73, 2008
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7EPS
 | | Partial Consensus L-threonine 3-dehydrogenase (E-change) | | Descriptor: | 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL, L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Kozuka, K, Nakano, S, Asano, Y, Ito, S. | | Deposit date: | 2021-04-27 | | Release date: | 2021-08-11 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.102 Å) | | Cite: | Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations.
Biochemistry, 60, 2021
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7EPR
 | | Partial Consensus L-threonine 3-dehydrogenase (C-Change) | | Descriptor: | L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | | Authors: | Kozuka, K, Nakano, S, Asano, Y, Ito, S. | | Deposit date: | 2021-04-27 | | Release date: | 2021-08-11 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations.
Biochemistry, 60, 2021
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7CGV
 | | Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ bound form) | | Descriptor: | Artificial L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | | Authors: | Motoyama, T, Hiramatsu, N, Asano, Y, Nakano, S, Ito, S. | | Deposit date: | 2020-07-02 | | Release date: | 2020-10-28 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | Protein Sequence Selection Method That Enables Full Consensus Design of Artificial l-Threonine 3-Dehydrogenases with Unique Enzymatic Properties.
Biochemistry, 59, 2020
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7CUO
 | | IclR transcription factor complexed with 4-hydroxybenzoic acid from Microbacterium hydrocarbonoxydans | | Descriptor: | P-HYDROXYBENZOIC ACID, SULFATE ION, Transcription factor | | Authors: | Akiyama, T, Ito, S, Sasaki, Y, Yajima, S. | | Deposit date: | 2020-08-23 | | Release date: | 2021-05-05 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding.
Biochim Biophys Acta Proteins Proteom, 1869, 2021
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7C4N
 | | Ancestral L-amino acid oxidase (AncLAAO-N5) L-Phe binding form | | Descriptor: | Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, PHENYLALANINE | | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | | Deposit date: | 2020-05-18 | | Release date: | 2020-12-02 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
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7C4L
 | | Anncestral L-amino acid oxidase (AncLAAO-N5) L-Gln binding form | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, GLUTAMINE, L-amino acid oxidase | | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | | Deposit date: | 2020-05-18 | | Release date: | 2020-12-02 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
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7C4M
 | | Ancestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form | | Descriptor: | Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, TRYPTOPHAN | | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | | Deposit date: | 2020-05-18 | | Release date: | 2020-12-02 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
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7C4K
 | | Ancestral L-amino acid oxidase (AncLAAO-N5) ligand free form | | Descriptor: | Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | | Deposit date: | 2020-05-18 | | Release date: | 2020-12-02 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
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3B0W
 | | Crystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with digoxin | | Descriptor: | DIGOXIN, Nuclear receptor ROR-gamma | | Authors: | Fujita-Sato, S, Ito, S, Isobe, T, Ohyama, T, Wakabayashi, K, Morishita, K, Ando, O, Isono, F. | | Deposit date: | 2011-06-17 | | Release date: | 2011-07-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural Basis of Digoxin That Antagonizes ROR{gamma}t Receptor Activity and Suppresses Th17 Cell Differentiation and Interleukin (IL)-17 Production
J.Biol.Chem., 286, 2011
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3VRH
 | | Crystal structure of ph0300 | | Descriptor: | BICINE, Putative uncharacterized protein PH0300, ZINC ION | | Authors: | Nakagawa, H, Kuratani, M, Goto-Ito, S, Ito, T, Sekine, S.I, Yokoyama, S. | | Deposit date: | 2012-04-10 | | Release date: | 2013-03-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.
Proteins, 2013
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8K9Y
 | | Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis | | Descriptor: | ADENOSINE-3'-5'-DIPHOSPHATE, CITRATE ANION, Cytosolic sulfotransferase 16, ... | | Authors: | Iwamoto, Y, Saito, S, Teramoto, T, Kakuta, Y. | | Deposit date: | 2023-08-02 | | Release date: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis.
Biochem.Biophys.Res.Commun., 677, 2023
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1EE6
 | | CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15. | | Descriptor: | CALCIUM ION, PECTATE LYASE | | Authors: | Akita, M, Suzuki, A, Kobayashi, T, Ito, S, Yamane, T. | | Deposit date: | 2000-01-31 | | Release date: | 2001-01-31 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The first structure of pectate lyase belonging to polysaccharide lyase family 3.
Acta Crystallogr.,Sect.D, 57, 2001
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1G01
 | | ALKALINE CELLULASE K CATALYTIC DOMAIN | | Descriptor: | ACETIC ACID, CADMIUM ION, ENDOGLUCANASE | | Authors: | Shirai, T, Ishida, H, Noda, J, Yamane, T, Ozaki, K, Hakamada, Y, Ito, S. | | Deposit date: | 2000-10-05 | | Release date: | 2001-08-01 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
J.Mol.Biol., 310, 2001
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1G0C
 | | ALKALINE CELLULASE K CATALYTIC DOMAIN-CELLOBIOSE COMPLEX | | Descriptor: | ACETIC ACID, CADMIUM ION, ENDOGLUCANASE, ... | | Authors: | Shirai, T, Ishida, H, Noda, J, Yamane, T, Ozaki, K, Hakamada, Y, Ito, S. | | Deposit date: | 2000-10-05 | | Release date: | 2001-08-01 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
J.Mol.Biol., 310, 2001
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2D22
 | | Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | | Descriptor: | ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, SULFATE ION, ... | | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | | Deposit date: | 2005-09-02 | | Release date: | 2006-10-10 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86
J.Biochem., 146, 2009
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2D1Z
 | | Crystal structure of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | | Descriptor: | ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, SULFATE ION | | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | | Deposit date: | 2005-09-02 | | Release date: | 2006-10-10 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86
J.Biochem., 146, 2009
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