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Yorodumi- PDB-7c83: Crystal structure of an integral membrane steroid 5-alpha-reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c83 | ||||||
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Title | Crystal structure of an integral membrane steroid 5-alpha-reductase PbSRD5A | ||||||
Components | 3-oxo-5-alpha-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / steroid reductase / NADPH / steroid 3-oxo-delta(4) reduction | ||||||
Function / homology | Function and homology information 3-oxo-5-alpha-steroid 4-dehydrogenase activity / steroid metabolic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Proteobacteria bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ren, R.B. / Han, Y.F. / Xiao, Q.J. / Deng, D. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism. Authors: Han, Y. / Zhuang, Q. / Sun, B. / Lv, W. / Wang, S. / Xiao, Q. / Pang, B. / Zhou, Y. / Wang, F. / Chi, P. / Wang, Q. / Li, Z. / Zhu, L. / Li, F. / Deng, D. / Chiang, Y.C. / Li, Z. / Ren, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c83.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c83.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 7c83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c83_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7c83_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7c83_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7c83_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/7c83 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/7c83 | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 29058.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteobacteria bacterium (bacteria) / Gene: DCC71_03205 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A3A0FWV3 | ||||
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#2: Chemical | ChemComp-NDP / | ||||
#3: Chemical | ChemComp-OLC / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 40% PEG 400, 100 mM HEPES pH 7.5, 100 mM potassium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.365 Å / Num. obs: 22993 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.844 / Num. unique obs: 1628 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREDICTED MODEL Resolution: 2→19.36 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.07 / 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: 84.92 Å2 / Biso mean: 35.99 Å2 / Biso min: 11.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→19.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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