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Yorodumi- PDB-3cot: Crystal structure of human liver delta(4)-3-ketosteroid 5beta-red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cot | ||||||
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Title | Crystal structure of human liver delta(4)-3-ketosteroid 5beta-reductase (akr1d1) in complex with progesterone and nadp. Resolution: 2.03 A. | ||||||
Components | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / steroid C-C double bond reduction / 5beta reductase / E120 / Bile acid catabolism / Cytoplasm / Disease mutation / Lipid metabolism / NADP / 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: 2.03 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 | 3cot.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cot.ent.gz | 122.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/3cot ftp://data.pdbj.org/pub/pdb/validation_reports/co/3cot | HTTPS FTP |
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-Related structure data
Related structure data | 3burSC 3buvC 3bv7C 3cmfC C: citing same article (ref.) S: Starting model for refinement |
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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: 39599.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / 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: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: isopropanol 10%,peg 4000, tris-HCl 100 mM 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: NSLS / Beamline: X29A / Wavelength: 1.008 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2008 Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 45518 / Num. obs: 44101 / % possible obs: 97.6 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.03→2.15 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / Num. unique all: 4301 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3bur Resolution: 2.03→25.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 71162.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.5085 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→25.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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