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Yorodumi- PDB-7e24: Crystal structure of SDR family NAD(P)-dependent oxidoreductase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+24 | ||||||
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Title | Crystal structure of SDR family NAD(P)-dependent oxidoreductase from Exiguobacterium | ||||||
Components | Oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / mutant / short chain reductase | ||||||
Function / homology | short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase Function and homology information | ||||||
Biological species | Exiguobacterium acetylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7203 Å | ||||||
Authors | Chen, L. / Tang, J. / Yuan, S. | ||||||
Citation | Journal: Catalysis Science And Technology / Year: 2021 Title: Structure-guided evolution of a ketoreductase forefficient and stereoselective bioreduction of bulkyalpha-aminobeta-keto esters Authors: Tang, J. / Chen, L. / Zhang, L. / Ni, G. / Yu, J. / Wang, H. / Zhang, F. / Yuan, S. / Feng, M. / Che, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e24.cif.gz | 201 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e24.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 7e24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/7e24 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e24 | HTTPS FTP |
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-Related structure data
Related structure data | 7e28C 7e3xC 5t2uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27454.092 Da / Num. of mol.: 4 Mutation: W82L,F88V, V121A, A138L, R142M, A190V, S193A, Y201F, N204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium acetylicum (bacteria) / Gene: ker / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6BDS0 #2: Chemical | ChemComp-NAP / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→34.08 Å / Num. obs: 30050 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.137 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.72→2.79 Å / Rmerge(I) obs: 0.534 / Num. unique obs: 2115 / CC1/2: 0.712 / Rpim(I) all: 0.513 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5t2u Resolution: 2.7203→17.2607 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 80.56 Å2 / Biso mean: 29.838 Å2 / Biso min: 11.61 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7203→17.2607 Å
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LS refinement shell | Resolution: 2.7203→2.8435 Å
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