5Y5M
 
 | | SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2018-08-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5L
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5I
 | | Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5YTL
 | | Crystal structure of Geobacillus thermodenitrificans copper-containing nitrite reductase determined with an anaerobically manipulated crystal | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, ACETIC ACID, ... | | Authors: | Fukuda, Y, Matsusaki, T, Tse, K.M, Mizohata, E, Murphy, M.E.P, Inoue, T. | | Deposit date: | 2017-11-19 | | Release date: | 2018-08-22 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.401 Å) | | Cite: | Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.
Acta Crystallogr D Struct Biol, 74, 2018
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5Y5J
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state) | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5K
 | | Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5YTN
 | | C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Fukuda, Y, Matsusaki, T, Tse, K.M, Mizohata, E, Murphy, M.E.P, Inoue, T. | | Deposit date: | 2017-11-19 | | Release date: | 2018-08-22 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.
Acta Crystallogr D Struct Biol, 74, 2018
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3WXS
 | | Thaumatin structure determined by SPring-8 Angstrom Compact free electron Laser (SACLA) | | Descriptor: | L(+)-TARTARIC ACID, thaumatin I | | Authors: | Masuda, T, Nango, E, Sugahara, M, Mizohata, E, Tanaka, T, Tanaka, R, Suzuki, M, Mikami, B, Iwata, S. | | Deposit date: | 2014-08-07 | | Release date: | 2014-11-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Grease matrix as a versatile carrier of proteins for serial crystallography
Nat. Methods, 12, 2015
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5YTM
 | | C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans determined by in-ouse source | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, ACETIC ACID, COPPER (II) ION, ... | | Authors: | Fukuda, Y, Matsusaki, T, Tse, K.M, Mizohata, E, Murphy, M.E.P, Inoue, T. | | Deposit date: | 2017-11-19 | | Release date: | 2018-08-22 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.
Acta Crystallogr D Struct Biol, 74, 2018
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5XDV
 | | Staphylococcus aureus FtsZ 12-316 G196S complexed with TXA6101 | | Descriptor: | 3-[[5-bromanyl-4-[4-(trifluoromethyl)phenyl]-1,3-oxazol-2-yl]methoxy]-2,6-bis(fluoranyl)benzamide, CALCIUM ION, Cell division protein FtsZ, ... | | Authors: | Fujita, J, Maeda, Y, Mizohata, E, Inoue, T, Kaul, M, Parhi, A.K, LaVoie, E.J, Pilch, D.S, Matsumura, H. | | Deposit date: | 2017-03-30 | | Release date: | 2017-08-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural Flexibility of an Inhibitor Overcomes Drug Resistance Mutations in Staphylococcus aureus FtsZ
ACS Chem. Biol., 12, 2017
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3WII
 | | Crystal structure of the Fab fragment of B2212A, a murine monoclonal antibody specific for the third fibronectin domain (Fn3) of human ROBO1. | | Descriptor: | anti-human ROBO1 antibody B2212A Fab heavy chain, anti-human ROBO1 antibody B2212A Fab light chain | | Authors: | Nakayama, T, Mizohata, E, Yamashita, T, Nagatoishi, S, Nakakido, M, Iwanari, H, Mochizuki, Y, Kado, Y, Yokota, Y, Sato, R, Tsumoto, K, Fujitani, H, Kodama, T, Hamakubo, T, Inoue, T. | | Deposit date: | 2013-09-12 | | Release date: | 2015-01-21 | | Last modified: | 2017-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Protein Sci., 24, 2015
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5YAE
 | | Ferulic acid esterase from Streptomyces cinnamoneus at 2.4 A resolution | | Descriptor: | ACETATE ION, Esterase, SULFATE ION | | Authors: | Tamura, H, Uraji, M, Mizohata, E, Ogawa, K, Inoue, T, Hatanaka, T. | | Deposit date: | 2017-08-31 | | Release date: | 2017-12-06 | | Last modified: | 2018-01-31 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass.
Appl. Environ. Microbiol., 84, 2018
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3WIH
 | | Crystal structure of the third fibronectin domain (Fn3) of human ROBO1 in complex with the Fab fragment of murine monoclonal antibody B2212A. | | Descriptor: | GLYCEROL, Roundabout homolog 1, anti-human ROBO1 antibody B2212A Fab heavy chain, ... | | Authors: | Nakayama, T, Mizohata, E, Yamashita, T, Nagatoishi, M, Iwanari, H, Mochizuki, Y, Kado, Y, Yokota, Y, Sato, R, Tsumoto, K, Fujitani, H, Kodama, T, Hamakubo, T, Inoue, T. | | Deposit date: | 2013-09-12 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Protein Sci., 24, 2015
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3WBG
 | | Structure of the human heart fatty acid-binding protein in complex with 1-anilinonaphtalene-8-sulphonic acid | | Descriptor: | 8-ANILINO-1-NAPHTHALENE SULFONATE, Fatty acid-binding protein, heart | | Authors: | Hirose, M, Sugiyama, S, Ishida, H, Niiyama, M, Matsuoka, D, Hara, T, Sato, F, Mizohata, E, Murakami, S, Inoue, T, Matsuoka, S, Murata, M. | | Deposit date: | 2013-05-16 | | Release date: | 2013-10-30 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid
J.SYNCHROTRON RADIAT., 20, 2013
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3WVM
 | | The 0.88 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with stearic acid | | Descriptor: | Fatty acid-binding protein, heart, HEXAETHYLENE GLYCOL, ... | | Authors: | Sugiyama, S, Matsuoka, S, Mizohata, E, Matsuoka, D, Ishida, H, Hirose, M, Kakinouchi, K, Hara, T, Matsumura, H, Murakami, S, Inoue, T, Murata, M. | | Deposit date: | 2014-05-25 | | Release date: | 2015-01-28 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (0.88 Å) | | Cite: | Water-mediated recognition of simple alkyl chains by heart-type fatty-acid-binding protein.
Angew.Chem.Int.Ed.Engl., 54, 2015
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3WYQ
 | | Crystal structure of the low-immunogenic core streptavidin mutant LISA-314 (Y22S/Y83S/R84K/E101D/R103K/E116N) at 1.0 A resolution | | Descriptor: | BIOTIN, GLYCEROL, SULFATE ION, ... | | Authors: | Kawato, T, Mizohata, E, Meshizuka, T, Doi, H, Kawamura, T, Matsumura, H, Yumura, K, Tsumoto, K, Kodama, T, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-09-05 | | Release date: | 2014-12-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Crystal structure of streptavidin mutant with low immunogenicity.
J.Biosci.Bioeng., 119, 2015
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3WYP
 | | Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution | | Descriptor: | BIOTIN, BIOTIN-D-SULFOXIDE, GLYCEROL, ... | | Authors: | Kawato, T, Mizohata, E, Meshizuka, T, Doi, H, Kawamura, T, Matsumura, H, Yumura, K, Tsumoto, K, Kodama, T, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-09-05 | | Release date: | 2014-12-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Crystal structure of streptavidin mutant with low immunogenicity.
J.Biosci.Bioeng., 119, 2015
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3WZN
 | | Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin at 1.3 A resolution | | Descriptor: | BIOTIN, SULFATE ION, Streptavidin | | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-10-01 | | Release date: | 2015-02-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.
J.Biochem., 157, 2015
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3WZP
 | | Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.2 A resolution | | Descriptor: | 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, GLYCEROL, Streptavidin | | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-10-01 | | Release date: | 2015-02-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.
J.Biochem., 157, 2015
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3WZQ
 | | Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.7 A resolution | | Descriptor: | 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, HEXAETHYLENE GLYCOL, Streptavidin | | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-10-01 | | Release date: | 2015-02-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.
J.Biochem., 157, 2015
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3WZO
 | | Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin long tail (BTNtail) at 1.5 A resolution | | Descriptor: | 6-({5-[(3aS,4S,5S,6aR)-5-oxido-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, CADMIUM ION, GLYCEROL, ... | | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-10-01 | | Release date: | 2015-02-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.
J.Biochem., 157, 2015
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3X00
 | | Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with bis iminobiotin long tail (Bis-IMNtail) at 1.3 A resolution | | Descriptor: | 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, ETHANE-1,2-DIAMINE, Streptavidin | | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-10-09 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant.
Biosci.Biotechnol.Biochem., 79, 2015
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5XDW
 | | Staphylococcus aureus FtsZ 12-316 G196S | | Descriptor: | CALCIUM ION, Cell division protein FtsZ, GUANOSINE-5'-DIPHOSPHATE | | Authors: | Fujita, J, Maeda, Y, Mizohata, E, Inoue, T, Kaul, M, Parhi, A.K, LaVoie, E.J, Pilch, D.S, Matsumura, H. | | Deposit date: | 2017-03-30 | | Release date: | 2017-08-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural Flexibility of an Inhibitor Overcomes Drug Resistance Mutations in Staphylococcus aureus FtsZ
ACS Chem. Biol., 12, 2017
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5X9S
 | | Crystal structure of fully modified H-Ras-GppNHp | | Descriptor: | CALCIUM ION, GTPase HRas, MAGNESIUM ION, ... | | Authors: | Matsumoto, S, Ke, H, Murashima, Y, Taniguchi-Tamura, H, Miyamoto, R, Yoshikawa, Y, Kumasaka, T, Mizohata, E, Edamatsu, H, Kataoka, T. | | Deposit date: | 2017-03-09 | | Release date: | 2017-08-30 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for intramolecular interaction of post-translationally modified H-RasGTP prepared by protein ligation
FEBS Lett., 591, 2017
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5YAL
 | | Ferulic acid esterase from Streptomyces cinnamoneus at 1.5 A resolution | | Descriptor: | ACETATE ION, Esterase, GLYCEROL, ... | | Authors: | Tamura, H, Uraji, M, Mizohata, E, Ogawa, K, Inoue, T, Hatanaka, T. | | Deposit date: | 2017-09-01 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass.
Appl. Environ. Microbiol., 84, 2018
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