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Yorodumi- PDB-3t1u: Crystal Structure of the complex of Cyclophilin-A enzyme from Azo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t1u | ||||||
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Title | Crystal Structure of the complex of Cyclophilin-A enzyme from Azotobacter vinelandii with sucAFPFpNA peptide | ||||||
Components |
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Keywords | ISOMERASE / peptidyl-prolyl isomerase / PPIase | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Karpusas, M. / Christoforides, E. / Bethanis, K. / Dimou, M. / Katinakis, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of a bacterial cytoplasmic cyclophilin A in complex with a tetrapeptide. Authors: Christoforides, E. / Dimou, M. / Katinakis, P. / Bethanis, K. / Karpusas, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t1u.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t1u.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t1u_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 3t1u_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 3t1u_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3t1u_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/3t1u ftp://data.pdbj.org/pub/pdb/validation_reports/t1/3t1u | HTTPS FTP |
-Related structure data
Related structure data | 1lopS 3t17 S: Starting model for refinement |
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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: 17681.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: Avin_23510 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1DHE4, peptidylprolyl isomerase |
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#2: Protein/peptide | Mass: 700.737 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 291.16 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 19% PEG8000, 0.1 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.16K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 11291 / % possible obs: 99.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.72 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.74 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LOP Resolution: 2→33.207 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 39.9094 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.52 Å2 / Biso mean: 25.4721 Å2 / Biso min: 10.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.207 Å
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Refine LS restraints |
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