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Yorodumi- PDB-3buv: Crystal structure of human Delta(4)-3-ketosteroid 5-beta-reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3buv | ||||||
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Title | Crystal structure of human Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and HEPES. Resolution: 1.35 A. | ||||||
Components | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 5-beta-reductase / catalytic tetrad / E120 / HEPES / NADP / Bile acid catabolism / Disease mutation / Lipid metabolism / Steroid metabolism | ||||||
Function / homology | Function and homology information Delta4-3-oxosteroid 5beta-reductase / C21-steroid hormone metabolic process / steroid dehydrogenase activity / bile acid catabolic process / delta4-3-oxosteroid 5beta-reductase activity / bile acid biosynthetic process / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / aldo-keto reductase (NADPH) activity / cholesterol catabolic process ...Delta4-3-oxosteroid 5beta-reductase / C21-steroid hormone metabolic process / steroid dehydrogenase activity / bile acid catabolic process / delta4-3-oxosteroid 5beta-reductase activity / bile acid biosynthetic process / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / aldo-keto reductase (NADPH) activity / cholesterol catabolic process / aldose reductase (NADPH) activity / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / steroid binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 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 | 3buv.cif.gz | 156.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3buv.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3buv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3buv ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3buv | HTTPS FTP |
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-Related structure data
Related structure data | 3burSC 3bv7C 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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1 |
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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 / Production host: Escherichia coli (E. coli) References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: 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: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10-20% wt/vol Peg 4000; 10% isopropanol; 100mM Hepes pH 7.5; 2.0 mM NADP, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 147700 / Num. obs: 147700 / % possible obs: 95.7 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.9 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BUR Resolution: 1.35→33.69 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 179622.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1837 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→33.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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