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Yorodumi- PDB-7wbc: Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wbc | ||||||
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Title | Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4S)-2-2-methyl-2,4-pentanediol | ||||||
Components | SDR family NAD(P)-dependent oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Hydroxysteroid dehydrogenase / Complex / NAD+ | ||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / : Function and homology information | ||||||
Biological species | Rhodococcus ruber (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shi, S.-C. / Zheng, Y.-C. / Xu, J.-H. / Li, C.-X. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4S)-2-2-methyl-2,4-pentanediol Authors: Shi, S.-C. / Zheng, Y.-C. / Xu, J.-H. / Li, C.-X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wbc.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbc.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 7wbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbc ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbc | HTTPS FTP |
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-Related structure data
Related structure data | 5jy1S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27430.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus ruber (bacteria) / Gene: DCN13_20495, F1734_22905 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U2VFT3 |
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-Non-polymers , 6 types, 346 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2-(N-Morpholino) ethane sulfonic acid, MgCl2, CaCl2, MPD, P3350, 2-(N-morpholino) ethane sulfonic acid, imidazole |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.3 Å / Num. obs: 30411 / % possible obs: 95.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.979 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 1560 / CC1/2: 0.978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JY1 Resolution: 2→33.3 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.82 Å2 / Biso mean: 26.0029 Å2 / Biso min: 14.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→33.3 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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