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- PDB-3cpo: Crystal structure of ketosteroid isomerase D40N with bound 2-fluo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cpo | ||||||
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Title | Crystal structure of ketosteroid isomerase D40N with bound 2-fluorophenol | ||||||
![]() | Delta(5)-3-ketosteroid isomerase | ||||||
![]() | ISOMERASE / ENZYME / ACTIVE SITE / HYDROGEN BOND / GEOMETRY / Lipid metabolism / Steroid metabolism | ||||||
Function / homology | ![]() steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Caaveiro, J.M.M. / Pybus, B. / Ringe, D. / Petsko, G. | ||||||
![]() | ![]() Title: Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole Authors: Sigala, P.A. / Kraut, D.A. / Caaveiro, J.M.M. / Pybus, B. / Ruben, E.A. / Ringe, D. / Petsko, G.A. / Herschlag, D. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.4 KB | Display | ![]() |
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PDB format | ![]() | 51.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2inxSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14547.515 Da / Num. of mol.: 1 / Mutation: D40N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FP2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: AMMONIUM SULPHATE 1.4 M, 2-PROPANOL 5-7%, PROTEIN CONCENTRATION 25 MG/ML, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→50 Å / Num. all: 33296 / Num. obs: 33296 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.053 / Χ2: 1.006 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.24→1.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 2335 / Χ2: 1.006 / % possible all: 67.7 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2INX Resolution: 1.24→36.19 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.591 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.999 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→36.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.274 Å / Total num. of bins used: 20
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