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Yorodumi- PDB-1e3v: Crystal structure of ketosteroid isomerase from Psedomonas putida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e3v | ||||||
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Title | Crystal structure of ketosteroid isomerase from Psedomonas putida complexed with deoxycholate | ||||||
Components | STEROID DELTA-ISOMERASE | ||||||
Keywords | ISOMERASE / DEOXYCHLATE / KSI / LBHB / REVERSE BINDING | ||||||
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 / OTHER / Resolution: 2 Å | ||||||
Authors | Ha, N.-C. / Kim, M.-S. / Kim, J.-S. / Oh, B.-H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Detection of Large Pka Perturbations of an Inhibitor and a Catalytic Group at an Enzyme Active Site, a Mechanistic Basis for Catalytic Power of Many Enzymes Authors: Ha, N.-C. / Kim, M.-S. / Lee, W. / 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 | 1e3v.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3v.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3v_validation.pdf.gz | 526 KB | Display | wwPDB validaton report |
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Full document | 1e3v_full_validation.pdf.gz | 529.3 KB | Display | |
Data in XML | 1e3v_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1e3v_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3v ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3v | HTTPS FTP |
-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.: 2 Source method: isolated from a genetically manipulated source Details: DEOXYCHOLATE / Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07445 #2: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.87 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 17811 / % possible obs: 92.7 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 97.69 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |