2UYR
| |
2DTM
| Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies | Descriptor: | IMMUNOGLOBULIN 6D9 | Authors: | Oda, M, Ito, N, Tsumuraya, T, Suzuki, K, Fujii, I. | Deposit date: | 2006-07-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis J.Mol.Biol., 369, 2007
|
|
7VGO
| Hen egg lysozyme | Descriptor: | CHLORIDE ION, Lysozyme C, SODIUM ION | Authors: | Oda, M, Ikura, T, Ito, N. | Deposit date: | 2021-09-17 | Release date: | 2022-02-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH. Protein J., 41, 2022
|
|
7VGP
| |
8IBL
| MES bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Alpha/beta hydrolase family protein, CALCIUM ION, ... | Authors: | Emori, M, Numoto, N, Kamiya, N, Oda, M. | Deposit date: | 2023-02-10 | Release date: | 2023-03-15 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism. Biorxiv, 2023
|
|
8IBM
| Sulfate bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, SULFATE ION | Authors: | Emori, M, Numoto, N, Kamiya, N, Oda, M. | Deposit date: | 2023-02-10 | Release date: | 2023-03-15 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism. Biorxiv, 2023
|
|
4H0V
| Crystal structure of NAD+-Ia(E378S)-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.03 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
4H03
| Crystal structure of NAD+-Ia-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-07 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
4H0X
| Crystal structure of NAD+-Ia(E380A)-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.33 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
4H0T
| Crystal structure of Ia-ADPR-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
4H0Y
| Crystal structure of NAD+-Ia(E380S)-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
8ISN
| HLA-A24 in complex with modified 9mer WT1 peptide | Descriptor: | Beta-2-microglobulin, CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU, GLYCEROL, ... | Authors: | Bekker, G.J, Numoto, N, Kawasaki, M, Hayashi, T, Yabuno, S, Kozono, Y, Shimizu, T, Kozono, H, Ito, N, Oda, M, Kamiya, N. | Deposit date: | 2023-03-21 | Release date: | 2023-09-13 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.48 Å) | Cite: | Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein Sci., 32, 2023
|
|
4GY2
| Crystal structure of apo-Ia-actin complex | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Actin, alpha skeletal muscle, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-05 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.71 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
5ZNO
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant in Ca(2+)-bound state | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL | Authors: | Numoto, N, Inaba, S, Yamagami, Y, Kamiya, N, Bekker, G.J, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-10 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.60264349 Å) | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle. Biochemistry, 57, 2018
|
|
5ZRS
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl adipate bound state | Descriptor: | 6-ethoxy-6-oxohexanoic acid, Alpha/beta hydrolase family protein, CALCIUM ION, ... | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-25 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle. Biochemistry, 57, 2018
|
|
5ZRR
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl succinate bound state | Descriptor: | 4-ethoxy-4-oxobutanoic acid, Alpha/beta hydrolase family protein, GLYCEROL, ... | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-25 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.34 Å) | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle. Biochemistry, 57, 2018
|
|
5ZRQ
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL, ... | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-25 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.12 Å) | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle. Biochemistry, 57, 2018
|
|
1VEA
| Crystal Structure of HutP, an RNA binding antitermination protein | Descriptor: | Hut operon positive regulatory protein, N-(2-NAPHTHYL)HISTIDINAMIDE | Authors: | Kumarevel, T.S, Fujimoto, Z, Karthe, P, Oda, M, Mizuno, H, Kumar, P.K.R. | Deposit date: | 2004-03-29 | Release date: | 2004-07-20 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal Structure of Activated HutP; An RNA Binding Protein that Regulates Transcription of the hut Operon in Bacillus subtilis Structure, 12, 2004
|
|
4WFJ
| Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 1.75 angstrom resolution | Descriptor: | CALCIUM ION, CHLORIDE ION, Cutinase | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | Deposit date: | 2014-09-15 | Release date: | 2014-12-24 | Last modified: | 2020-01-29 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190. Appl.Microbiol.Biotechnol., 99, 2015
|
|
4WFK
| Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 2.35 angstrom resolution | Descriptor: | CALCIUM ION, CHLORIDE ION, Cutinase | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | Deposit date: | 2014-09-15 | Release date: | 2014-12-24 | Last modified: | 2020-01-29 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190. Appl.Microbiol.Biotechnol., 99, 2015
|
|
4WFI
| Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-free state | Descriptor: | Cutinase | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | Deposit date: | 2014-09-15 | Release date: | 2014-12-24 | Last modified: | 2020-01-29 | Method: | X-RAY DIFFRACTION (1.446 Å) | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190. Appl.Microbiol.Biotechnol., 99, 2015
|
|
2DDS
| Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion | Descriptor: | COBALT (II) ION, Sphingomyelin phosphodiesterase | Authors: | Ago, H, Oda, M, Takahashi, M, Tsuge, H, Ochi, S, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-02-02 | Release date: | 2006-05-02 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus. J.Biol.Chem., 281, 2006
|
|
1IDZ
| |
1IDY
| |
2DDR
| Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion | Descriptor: | CALCIUM ION, Sphingomyelin phosphodiesterase | Authors: | Ago, H, Oda, M, Takahashi, M, Tsuge, H, Ochi, S, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-02-02 | Release date: | 2006-05-02 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus. J.Biol.Chem., 281, 2006
|
|