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Yorodumi- PDB-3ows: Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ows | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M116C-CN from P. putida with Bound Equilenin | ||||||
Components | Steroid Delta-isomerase | ||||||
Keywords | ISOMERASE / Steroid / Cyanylation | ||||||
Function / homology | Function and homology information steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Sigala, P.A. / Fenn, T.D. / Herschlag, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Authors: Sigala, P.A. / Fafarman, A.T. / Schwans, J.P. / Fried, S.D. / Fenn, T.D. / Caaveiro, J.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Boxer, S.G. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ows.cif.gz | 218.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ows.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ows.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/3ows ftp://data.pdbj.org/pub/pdb/validation_reports/ow/3ows | HTTPS FTP |
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-Related structure data
Related structure data | 3vgnC 2pzvS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14496.276 Da / Num. of mol.: 4 / Mutation: D40N, C69S, C81S, C97S, M116(XCN) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase #2: Chemical | ChemComp-EQU / #3: 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: 2.16 Å3/Da / Density % sol: 43.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.1 M ammonium sulfate, 5% isopropanol, 40 mM potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→36.41 Å / Num. all: 52970 / Num. obs: 41740 / % possible obs: 79 % / Biso Wilson estimate: 11.58 Å2 |
Reflection shell | Resolution: 1.71→1.75 Å / % possible all: 17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PZV Resolution: 1.71→36.41 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7656 / SU ML: 1.44 / Cross valid method: THROUGHOUT / σ(F): 0.03 / 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: 50.623 Å2 / ksol: 0.42 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.34 Å2 / Biso mean: 28.8616 Å2 / Biso min: 5.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→36.41 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: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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