+Open data
-Basic information
Entry | Database: PDB / ID: 1e3b | ||||||
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Title | CYCLOPHILIN 3 FROM C.ELEGANS COMPLEXED WITH AUP(ET)3 | ||||||
Components | CYCLOPHILIN 3 | ||||||
Keywords | ISOMERASE / AUPET3 ADDUCT CYCLOPHILIN ANTIARTHRITIC GOLD | ||||||
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: 1.85 Å | ||||||
Authors | Zou, J. / Taylor, P. / Dornan, J. / Robinson, S.P. / Walkinshaw, M.D. / Sadler, P.J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2000 Title: First Crystal Structure of a Medicinally Relevant Gold Protein Complex:Unexpected Binding of [Au(Pet (3))](+) to Histidine Authors: Zou, J. / Taylor, P. / Dornan, J. / Robinson, S.P. / Walkinshaw, M.D. / Sadler, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3b.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3b.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3b_validation.pdf.gz | 376.7 KB | Display | wwPDB validaton report |
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Full document | 1e3b_full_validation.pdf.gz | 380.6 KB | Display | |
Data in XML | 1e3b_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1e3b_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3b ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3b | HTTPS FTP |
-Related structure data
Similar structure data |
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-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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52011 |
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#2: Chemical | ChemComp-AU / |
#3: Chemical | ChemComp-3EP / |
#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: 2.63 Å3/Da / Density % sol: 60.29 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: HANGING DROP PH5.6 15.5% W/V MPEG 5000, 50 MM SODIUM CITRATE. WELL SOLUTION: 31% MPEG 5000, 100MM SODIUM CITRATE, pH 5.60 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: PX9.5 / Wavelength: 1.3 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 17, 1999 / Details: PT COATED TORROIDAL MIRRO |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→35 Å / Num. obs: 20154 / % possible obs: 98.3 % / Redundancy: 4.12 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.03 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 9.92 / % possible all: 1 |
Reflection | *PLUS Num. measured all: 185907 |
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CYCLOPHILIN 3 NATIVE Resolution: 1.85→31 Å / Num. parameters: 6117 / Num. restraintsaints: 5315 / Cross valid method: FREE R-VALUE / σ(F): 0 StereochEM target val spec case: AU PET3 PARAMETERS CALCULATED FROM SMALL MOLECULE DATABASE (CCDC) Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1526 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→31 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.036 |