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Yorodumi- PDB-1vai: Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vai | ||||||
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Title | Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin | ||||||
Components |
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Keywords | ISOMERASE / BETA BARREL | ||||||
Function / homology | Function and homology information protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Konno, M. / Sano, Y. / Okudaira, K. / Kawaguchi, Y. / Yamagishi-Ohmori, Y. / Fushinobu, S. / Matsuzawa, H. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2004 Title: Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer Authors: Konno, M. / Sano, Y. / Okudaira, K. / Kawaguchi, Y. / Yamagishi-Ohmori, Y. / Fushinobu, S. / Matsuzawa, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vai.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vai.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vai_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 1vai_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 1vai_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1vai_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vai ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vai | HTTPS FTP |
-Related structure data
Related structure data | 1j2aC 1v9tSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 18070.326 Da / Num. of mol.: 2 / Mutation: K163T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PATRP EPPIA / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P20752, UniProt: P0AFL3*PLUS, peptidylprolyl isomerase #2: Protein/peptide | ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: AMMONIUM SULPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 20, 1998 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→80 Å / Num. obs: 35961 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.8→1.88 Å / Rmerge(I) obs: 0.371 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 1V9T Resolution: 1.8→6 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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