7E4D
 
 | | Crystal structure of PlDBR | | Descriptor: | Double Bond Reductase | | Authors: | Sugimoto, K, Senda, M, Senda, T. | | Deposit date: | 2021-02-11 | | Release date: | 2022-02-02 | | Last modified: | 2022-03-02 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Exploration and structure-based engineering of alkenal double bond reductases catalyzing the C alpha C beta double bond reduction of coniferaldehyde.
N Biotechnol, 68, 2022
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7EM6
 | | Crystal structure of the PI5P4Kbeta N203D-ITP complex | | Descriptor: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM2
 | | Crystal structure of the PI5P4Kbeta-XTP complex | | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM1
 | | Crystal structure of the PI5P4Kbeta-ITP complex | | Descriptor: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM7
 | | Crystal structure of the PI5P4Kbeta N203D-XTP complex | | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.45 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM5
 | | Crystal structure of the PI5P4Kbeta F205L-XTP complex | | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM3
 | | Crystal structure of the PI5P4Kbeta-2a-ATP complex | | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM4
 | | Crystal structure of the PI5P4Kbeta F205L-ITP complex | | Descriptor: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM8
 | | Crystal structure of the PI5P4Kbeta T201M-2a-ATP complex | | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.05 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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3A2M
 | | CRYSTAL STRUCTURE OF DBJA (WILD TYPE Type I) | | Descriptor: | CHLORIDE ION, Haloalkane dehalogenase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2009-05-23 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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3A2L
 | | Crystal structure of DBJA (mutant dbja delta) | | Descriptor: | CHLORIDE ION, GLYCEROL, Haloalkane dehalogenase, ... | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2009-05-23 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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3AFI
 | | Crystal structure of DBJA (HIS-DBJA) | | Descriptor: | CHLORIDE ION, Haloalkane dehalogenase | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2010-03-02 | | Release date: | 2011-01-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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3A2N
 | | Crystal structure of DBJA (Wild Type Type II P21) | | Descriptor: | CHLORIDE ION, Haloalkane dehalogenase | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2009-05-23 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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5XNY
 | | Crystal structure of CreD | | Descriptor: | CreD | | Authors: | Katsuyama, Y, Sato, Y, Sugai, Y, Higashiyama, Y, Senda, M, Senda, T, Ohnishi, Y. | | Deposit date: | 2017-05-25 | | Release date: | 2018-03-14 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
FEBS J., 285, 2018
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5XNZ
 | | Crystal structure of CreD complex with fumarate | | Descriptor: | CreD, FUMARIC ACID | | Authors: | Katsuyama, Y, Sato, Y, Sugai, Y, Higashiyama, Y, Senda, M, Senda, T, Ohnishi, Y. | | Deposit date: | 2017-05-25 | | Release date: | 2018-03-14 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
FEBS J., 285, 2018
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6M3X
 | | Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii | | Descriptor: | FE (III) ION, Sulfur oxygenase/reductase | | Authors: | Sato, Y, Adachi, N, Moriya, T, Arakawa, T, Kawasaki, M, Yamada, C, Senda, T, Fushinobu, S. | | Deposit date: | 2020-03-04 | | Release date: | 2020-07-15 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (2.24 Å) | | Cite: | Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase fromSulfurisphaera tokodaii.
J Struct Biol X, 4, 2020
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6KNF
 | | CryoEM map and model of Nitrite Reductase at pH 6.2 | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase | | Authors: | Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-12 | | Last modified: | 2021-08-25 | | Method: | ELECTRON MICROSCOPY (2.99 Å) | | Cite: | 2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213, 2021
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6KFQ
 | | Crystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus | | Descriptor: | RETINAL, Rhodopsin, SULFATE ION, ... | | Authors: | Suzuki, K, Akiyama, T, Hayashi, T, Yasuda, S, Kanehara, K, Kojima, K, Tanabe, M, Kato, R, Senda, T, Sudo, Y, Kinoshita, M, Murata, T. | | Deposit date: | 2019-07-08 | | Release date: | 2020-04-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?
J.Phys.Chem.B, 124, 2020
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6KNG
 | | CryoEM map and model of Nitrite Reductase at pH 8.1 | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase | | Authors: | Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-12 | | Last modified: | 2021-08-25 | | Method: | ELECTRON MICROSCOPY (2.85 Å) | | Cite: | 2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213, 2021
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6KEM
 | | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in apo-form 2 | | Descriptor: | Glutathione S-transferase E14 | | Authors: | Koiwai, K, Inaba, K, Morohashi, K, Yumoto, F, Niwa, R, Senda, T. | | Deposit date: | 2019-07-04 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.
J.Biol.Chem., 295, 2020
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6KEL
 | | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in apo-form | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Glutathione S-transferase E14 | | Authors: | Koiwai, K, Inaba, K, Morohashi, K, Yumoto, F, Senda, T, Niwa, R. | | Deposit date: | 2019-07-04 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.
J.Biol.Chem., 295, 2020
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6KEQ
 | | Crystal structure of D113A mutant of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in apo-form | | Descriptor: | Glutathione S-transferase E14 | | Authors: | Koiwai, K, Inaba, K, Morohashi, K, Yumoto, F, Niwa, R, Senda, T. | | Deposit date: | 2019-07-04 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.
J.Biol.Chem., 295, 2020
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6KER
 | | Crystal structure of D113A mutant of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in glutathione-bound form | | Descriptor: | GLUTATHIONE, Glutathione S-transferase E14 | | Authors: | Koiwai, K, Inaba, K, Morohashi, K, Yumoto, F, Niwa, R, Senda, T. | | Deposit date: | 2019-07-04 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.
J.Biol.Chem., 295, 2020
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6KEN
 | | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in glutathione-bound form | | Descriptor: | GLUTATHIONE, Glutathione S-transferase E14 | | Authors: | Koiwai, K, Inaba, K, Morohashi, K, Yumoto, F, Niwa, R, Senda, T. | | Deposit date: | 2019-07-04 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.
J.Biol.Chem., 295, 2020
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7D98
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