+Open data
-Basic information
Entry | Database: PDB / ID: 1iip | ||||||
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Title | Bovine Cyclophilin 40, Tetragonal Form | ||||||
Components | Cyclophilin 40 | ||||||
Keywords | ISOMERASE / PPIASE IMMUNOPHILIN TETRATRICOPEPTIDE | ||||||
Function / homology | Function and homology information cellular response to UV-A / lipid droplet organization / cyclosporin A binding / transcription factor binding / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / Hsp70 protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity ...cellular response to UV-A / lipid droplet organization / cyclosporin A binding / transcription factor binding / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / Hsp70 protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / nuclear estrogen receptor binding / Hsp90 protein binding / protein transport / protein folding / protein-containing complex assembly / positive regulation of apoptotic process / apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Taylor, P. / Dornan, J. / Carrello, A. / Minchin, R.F. / Ratajczak, T. / Walkinshaw, M.D. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Two structures of cyclophilin 40: folding and fidelity in the TPR domains. Authors: Taylor, P. / Dornan, J. / Carrello, A. / Minchin, R.F. / Ratajczak, T. / Walkinshaw, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iip.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iip.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 1iip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iip_validation.pdf.gz | 378.9 KB | Display | wwPDB validaton report |
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Full document | 1iip_full_validation.pdf.gz | 389.2 KB | Display | |
Data in XML | 1iip_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1iip_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1iip ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1iip | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 40678.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26882, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 62.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPD, Imidazole glycerol Tris Sodium Chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 1999 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→28 Å / Num. all: 37488 / Num. obs: 37488 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.62 % / Biso Wilson estimate: 26.554 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.65 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.15 / % possible all: 90.5 |
Reflection | *PLUS Num. obs: 33904 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CYCLOPHILIN A Resolution: 2→24 Å / Num. parameters: 9975 / Num. restraintsaints: 9240 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2493 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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