+Open data
-Basic information
Entry | Database: PDB / ID: 1opy | ||||||
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Title | KSI | ||||||
Components | DELTA5-3-KETOSTEROID IOSMERASE | ||||||
Keywords | ISOMERASE / KSI / HIGH RESOLUTION / PSEUDOMONAS PUTIDA BIOTYPE B / LOW-BARRIER HYDROGEN BOND | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Kim, S.-W. / Cha, S.-S. / Cho, H.-S. / Kim, J.-S. / Ha, N.-C. / Cho, M.-J. / Choi, K.-Y. / Oh, B.-H. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue. Authors: Kim, S.W. / Cha, S.S. / Cho, H.S. / Kim, J.S. / Ha, N.C. / Cho, M.J. / Joo, S. / Kim, K.K. / Choi, K.Y. / Oh, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1opy.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1opy.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 1opy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1opy ftp://data.pdbj.org/pub/pdb/validation_reports/op/1opy | 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: 14548.501 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: BIOTYPE B / Plasmid: DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % | |||||||||||||||
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Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 11, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 6679 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Highest resolution: 1.9 Å |
-Processing
Software |
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Refinement | Resolution: 1.9→10 Å / σ(F): 1
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |