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Yorodumi- PDB-4xo7: Crystal structure of human 3-alpha hydroxysteroid dehydrogenase t... -
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-Basic information
Entry | Database: PDB / ID: 4xo7 | ||||||
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Title | Crystal structure of human 3-alpha hydroxysteroid dehydrogenase type 3 in complex with NADP+, 5alpha-androstan-3,17-dione and (3beta, 5alpha)-3-hydroxyandrostan-17-one | ||||||
Components | Aldo-keto reductase family 1 member C2 | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA BARREL / HUMAN 3-ALPHA HDS3 / AKR / AKR1C2 / ALDO-KETO REDUCTASE / NADPH | ||||||
Function / homology | Function and homology information indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase ...indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / carboxylic acid binding / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Oxidoreductases / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / aldose reductase (NADPH) activity / digestion / prostaglandin metabolic process / steroid metabolic process / epithelial cell differentiation / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Zhang, B. / Hu, X.-J. / Lin, S.-X. | ||||||
Citation | Journal: Biochem.J. / Year: 2016 Title: Human 3 alpha-hydroxysteroid dehydrogenase type 3: structural clues of 5 alpha-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth. Authors: Zhang, B. / Hu, X.J. / Wang, X.Q. / Theriault, J.F. / Zhu, D.W. / Shang, P. / Labrie, F. / Lin, S.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xo7.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xo7.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xo7_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4xo7_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4xo7_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 4xo7_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/4xo7 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xo7 | HTTPS FTP |
-Related structure data
Related structure data | 4xo6C 4nnf 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 2 - 323 / Label seq-ID: 2 - 323
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-Components
#1: Protein | Mass: 36786.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C2, DDH2 / Production host: Escherichia coli (E. coli) References: UniProt: P52895, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, 3alpha-hydroxysteroid 3-dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% PEG3350, 0.1M SODIUM CACODYLATE, 0.2M AMMONIUM SULFATE, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2012 |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. obs: 66677 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.2 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.019 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.108 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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