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Yorodumi- PDB-1c5f: CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c5f | |||||||||
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Title | CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A | |||||||||
Components |
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Keywords | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN | |||||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | BRUGIA MALAYI (agent of lymphatic filariasis) TOLYPOCLADIUM INFLATUM (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | |||||||||
Authors | Ellis, P.J. / Carlow, C.K.S. / Ma, D. / Kuhn, P. | |||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal Structure of the Complex of Brugia Malayi Cyclophilin and Cyclosporin A. Authors: Ellis, P.J. / Carlow, C.K. / Ma, D. / Kuhn, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c5f.cif.gz | 293.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c5f.ent.gz | 244.3 KB | Display | PDB format |
PDBx/mmJSON format | 1c5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c5f_validation.pdf.gz | 542.9 KB | Display | wwPDB validaton report |
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Full document | 1c5f_full_validation.pdf.gz | 570.3 KB | Display | |
Data in XML | 1c5f_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 1c5f_validation.cif.gz | 78.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c5f ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c5f | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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-Components
#1: Protein | Mass: 19504.418 Da / Num. of mol.: 8 / Fragment: CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BRUGIA MALAYI (agent of lymphatic filariasis) Gene: BMCYP-1 / Plasmid: PMAL-C2 / Gene (production host): MBP FUSION PROTEIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2267 / References: UniProt: Q27450, peptidylprolyl isomerase #2: Protein/peptide | Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 8 / Source method: obtained synthetically Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A #3: Water | ChemComp-HOH / | Compound details | CYCLOSPORI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.83 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→47.14 Å / Num. obs: 56200 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.47→2.53 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.372 / % possible all: 73.1 |
Reflection | *PLUS % possible obs: 77.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Num. measured all: 409247 / Rmerge(I) obs: 0.12 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→47.1 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: USED MAXIMUM LIKELIHOOD TARGET BASED ON STRUCTURE FACTORS WITH NO CUTOFFS
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Solvent computation | Bsol: 31.56 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→47.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.47→2.58 Å / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 47.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |