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Yorodumi- PDB-3uzw: Crystal structure of 5beta-reductase (AKR1D1) E120H mutant in com... -
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-Basic information
Entry | Database: PDB / ID: 3uzw | ||||||
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Title | Crystal structure of 5beta-reductase (AKR1D1) E120H mutant in complex with NADP+ | ||||||
Components | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ALDO-KETO REDUCTASE / STEROID AND BILE ACID METABOLISM / CATALYTIC TETRAD MUTANT / Tim Barrel | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.892 Å | ||||||
Authors | Chen, M. / Christianson, D.W. / Penning, T.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Conversion of Human Steroid 5beta-Reductase (AKR1D1) into 3β-Hydroxysteroid Dehydrogenase by Single Point Mutation E120H: EXAMPLE OF PERFECT ENZYME ENGINEERING. Authors: Chen, M. / Drury, J.E. / Christianson, D.W. / Penning, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uzw.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uzw.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 3uzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/3uzw ftp://data.pdbj.org/pub/pdb/validation_reports/uz/3uzw | HTTPS FTP |
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-Related structure data
Related structure data | 3uzxC 3uzyC 3uzzC 3bv7S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39608.289 Da / Num. of mol.: 2 / Mutation: E120H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / Plasmid: PET28A-AKR1D1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) 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: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-HCl, 14-20% polyethylene glycol 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: 24-ID-C / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.892→50 Å / Num. all: 57706 / Num. obs: 57071 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.114 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BV7 Resolution: 1.892→37.288 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8754 / SU ML: 0.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 19.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.56 Å2 / ksol: 0.311 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.37 Å2 / Biso mean: 18.8183 Å2 / Biso min: 3.59 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.892→37.288 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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