+Open data
-Basic information
Entry | Database: PDB / ID: 2ck1 | ||||||
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Title | The structure of oxidised cyclophilin A from s. mansoni | ||||||
Components | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E | ||||||
Keywords | ISOMERASE / DISULPHIDE BRIDGE / CYCLOPHILIN / CYCLOSPORIN / ROTAMASE ACTIVITY / ROTAMASE / RNA-BINDING / BETA-BARREL | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | SCHISTOSOMA MANSONI (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gourlay, L.J. / Angelucci, F. / Bellelli, A. / Boumis, G. / Miele, A.E. / Brunori, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The Three-Dimensional Structure of Two Redox States of Cyclophilin-A from Schistosoma Mansoni: Evidence for Redox- Regulation of Peptidyl-Prolyl Cis-Trans Isomerase Activity. Authors: Gourlay, L.J. / Angelucci, F. / Baiocco, P. / Boumis, G. / Brunori, M. / Bellelli, A. / Miele, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ck1.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ck1.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ck1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ck1_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 2ck1_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 2ck1_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2ck1_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/2ck1 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/2ck1 | HTTPS FTP |
-Related structure data
Related structure data | 2cmtC 1zmfS 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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Unit cell |
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-Components
#1: Protein | Mass: 19218.100 Da / Num. of mol.: 1 / Fragment: RESIDUES 102-273 Source method: isolated from a genetically manipulated source Details: DISULPHIDE BRINDGE BETWEEN C122 AND C126 / Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q26548, peptidylprolyl isomerase | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | PPIASES ACCELERATEHas protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 31.78 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 2.5% GLYCEROL, 30% PEG5K MME, 2UM COPPER (II) SULPHATE, 0.1M SODIUM ACETATE PH 5.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 227195 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.8 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZMF Resolution: 1.8→42.68 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.406 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.127 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→42.68 Å
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Refine LS restraints |
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