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Yorodumi- PDB-8kcn: X-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kcn | ||||||
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Title | X-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase mutant | ||||||
Components | NADP-dependent (R)-specific alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lactobacillaceae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Song, S.K. / Ma, Q.Q. / Lv, D.Q. / Cheng, C.Y. / Su, Z.D. | ||||||
Funding support | 1items
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Citation | Journal: to be published Title: X-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase mutant Authors: Song, S.K. / Ma, Q.Q. / Lv, D.Q. / Cheng, X.Y. / Su, Z.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kcn.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kcn.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 8kcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kcn_validation.pdf.gz | 408.5 KB | Display | wwPDB validaton report |
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Full document | 8kcn_full_validation.pdf.gz | 408.4 KB | Display | |
Data in XML | 8kcn_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 8kcn_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/8kcn ftp://data.pdbj.org/pub/pdb/validation_reports/kc/8kcn | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
#1: Protein | Mass: 26680.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillaceae (bacteria) / Gene: adh / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6WVP7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 30% PEG MME550; 0.1M Tris pH7.0; 0.05M MgCL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2023 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→65.365 Å / Num. obs: 60439 / % possible obs: 98.9 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.31→1.31 Å / Rmerge(I) obs: 0.1624 / Num. unique obs: 57490 / Rrim(I) all: 0.1792 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→31.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.586 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.18 Å2
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Refinement step | Cycle: 1 / Resolution: 1.31→31.47 Å
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Refine LS restraints |
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