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Yorodumi- PDB-2pzv: Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pzv | |||||||||
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Title | Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol | |||||||||
Components | Steroid Delta-isomerase | |||||||||
Keywords | ISOMERASE / transition state analog bound | |||||||||
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: 1.25 Å | |||||||||
Authors | Pybus, B. / Caaveiro, J.M.M. / Petsko, G.A. / Ringe, D. | |||||||||
Citation | Journal: PLoS Biol. / Year: 2006 Title: Testing Electrostatic complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole Authors: Kraut, D.A. / Sigala, P.A. / Pybus, B. / Liu, C.W. / Ringe, D. / Petsko, G.A. / Herschlag, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pzv.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pzv.ent.gz | 179.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/2pzv ftp://data.pdbj.org/pub/pdb/validation_reports/pz/2pzv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 14547.515 Da / Num. of mol.: 4 / Mutation: D40N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pKK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase #2: Chemical | ChemComp-IPH / #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: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.4 M ammonium sulphate, 7% (v/v) 2-propanol, 40 mM potasium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. all: 119468 / Num. obs: 111105 / % possible obs: 93 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.415 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→22.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.344 / SU ML: 0.044 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: hydrogens have been added in the riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→22.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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