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Yorodumi- PDB-3bv7: Crystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bv7 | ||||||
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Title | Crystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and glycerol. Resolution: 1.79 A. | ||||||
Components | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 5-beta-reductase / glycerol / AKR1A1 / Bile acid catabolism / Disease mutation / Lipid metabolism / NADP / Steroid metabolism | ||||||
Function / homology | Function and homology information Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid catabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / aldo-keto reductase (NADPH) activity / aldose reductase (NADPH) activity ...Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid catabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / aldo-keto reductase (NADPH) activity / aldose reductase (NADPH) activity / digestion / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cholesterol catabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / steroid binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.79 Å | ||||||
Authors | Di Costanzo, L. / Drury, J. / Penning, T.M. / Christianson, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal Structure of Human Liver {Delta}4-3-Ketosteroid 5{beta}-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis. Authors: Di Costanzo, L. / Drury, J.E. / Penning, T.M. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bv7.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bv7.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bv7_validation.pdf.gz | 989.7 KB | Display | wwPDB validaton report |
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Full document | 3bv7_full_validation.pdf.gz | 1008.5 KB | Display | |
Data in XML | 3bv7_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 3bv7_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bv7 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bv7 | HTTPS FTP |
-Related structure data
Related structure data | 3burSC 3buvC 3cmfC 3cotC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37427.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / Organ: liver / Plasmid: pET28a-AKR1D1 / Production host: Escherichia coli (E. coli) References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein: 5.0 mg/mL AKR1D1, 2.0 mM NADPH, 2.0 mM 5-beta-cholestan-3-one, 10.0 mM Tris (pH 7.4). Precipitant buffer: 0.1 M Tris (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% isopropanol., pH 7.5, ...Details: Protein: 5.0 mg/mL AKR1D1, 2.0 mM NADPH, 2.0 mM 5-beta-cholestan-3-one, 10.0 mM Tris (pH 7.4). Precipitant buffer: 0.1 M Tris (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% isopropanol., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2007 Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. all: 66774 / Num. obs: 66774 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6684 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BUR Resolution: 1.79→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.79→50 Å
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Refine LS restraints |
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