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Yorodumi- PDB-5kp3: Crystal Structure of Ketosteroid Isomerase from Pseudomonas putid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kp3 | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI) bound to Equilenin; D40N, Y57(Cl-Y) | ||||||
Components | Steroid Delta-isomerase | ||||||
Keywords | ISOMERASE | ||||||
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 / Resolution: 1.7 Å | ||||||
Authors | Wu, Y. / Boxer, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase. Authors: Wu, Y. / Boxer, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kp3.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kp3.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kp3 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kp3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15048.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase #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: 1.98 Å3/Da / Density % sol: 37.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.1-1.4M ammonium sulfate, 40mM potassium phosphate, 3-6% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→57.921 Å / Num. all: 27157 / Num. obs: 27157 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 19.75 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.084 / Rsym value: 0.074 / Net I/av σ(I): 4.647 / Net I/σ(I): 9.8 / Num. measured all: 109372 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.7→47.405 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.06 Å2 / Biso mean: 30.2808 Å2 / Biso min: 10.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→47.405 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: 10
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