+Open data
-Basic information
Entry | Database: PDB / ID: 2igw | ||||||
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Title | CYCLOPHILIN 3 complexed with DIPEPTIDE GLY-PRO | ||||||
Components | Peptidyl-prolyl cis-trans isomerase 3 | ||||||
Keywords | ISOMERASE / ROTAMASE | ||||||
Function / homology | Function and homology information cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Kan, D. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007 Title: Experimental Determination of van der Waals Energies in a Biological System. Authors: Wear, M.A. / Kan, D. / Rabu, A. / 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 | 2igw.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2igw.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 2igw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2igw ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2igw | HTTPS FTP |
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-Related structure data
Related structure data | 2igvC 1e8kS 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: 18576.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: PET-5A / Production host: Escherichia coli (E. coli) / References: UniProt: P52011, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-PRO / |
#4: 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: 3.25 Å3/Da / Density % sol: 61.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% MPEG 5000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9795 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→36.04 Å / Num. obs: 23790 / % possible obs: 98 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.01424 / Mean I/σ(I) obs: 0.9 / Num. unique all: 3131 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E8K Resolution: 1.78→35.95 Å / Num. parameters: 5688 / Num. restraintsaints: 5371 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1436.93 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→35.95 Å
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Refine LS restraints |
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