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Yorodumi- PDB-3caq: Crystal structure of 5beta-reductase (AKR1D1) in complex with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 3caq | ||||||
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Title | Crystal structure of 5beta-reductase (AKR1D1) in complex with NADPH | ||||||
Components | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 5b-reductase / 5beta-reductase / 5b-red / AKR1D1 / AKR / aldo-keto reductase / NADP / androstenedione / NADPH / 5b-dhp / substrate inhibition / Bile acid catabolism / Cytoplasm / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Faucher, F. / Cantin, L. / Breton, R. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal Structures of Human Delta4-3-Ketosteroid 5beta-Reductase (AKR1D1) Reveal the Presence of an Alternative Binding Site Responsible for Substrate Inhibition (dagger) (,) (double dagger). Authors: Faucher, F. / Cantin, L. / Luu-The, V. / Labrie, F. / Breton, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3caq.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3caq.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 3caq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3caq ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3caq | HTTPS FTP |
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-Related 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
-Protein , 1 types, 2 molecules AB
#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 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase |
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-Non-polymers , 5 types, 287 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.43 Å3/Da / Density % sol: 49.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG-4000 20%, 0.1M Tris, 5% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å | |||||||||||||||
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 7, 2007 / Details: mirrors | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.2→19.67 Å / Num. all: 37913 / Num. obs: 36835 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.973 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.074 / Net I/σ(I): 16.08 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 4.8 / Num. measured obs: 15843 / Num. unique all: 4644 / Num. unique obs: 4477 / Rsym value: 0.287 / % possible all: 96.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2673653 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.14 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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