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Open data
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Basic information
Entry | Database: PDB / ID: 1xo7 | ||||||
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Title | Crystal structure of cyclophilin from Trypanosoma cruzi | ||||||
![]() | cyclophilin | ||||||
![]() | ISOMERASE / cyclophilin / rotamase / proline / cis-trans / trypanosoma / cruzi / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM / SGPP | ||||||
Function / homology | ![]() peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caruthers, J.M. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
![]() | ![]() Title: Crystal structure of cyclophilin from Trypanosoma cruzi Authors: Caruthers, J.M. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN ANY REFERENCE SEQUENCE DATABASE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.1 KB | Display | ![]() |
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PDB format | ![]() | 122 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 54.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dywS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Details | putative monomer |
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Components
#1: Protein | Mass: 18057.537 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Ammonium Phosphate monobasic, Sodium Acetate, PEG8000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 25K, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2004 / Details: custom |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→56.8 Å / Num. all: 80854 / Num. obs: 80854 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rsym value: 0.103 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.61→1.7 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.55 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DYW.pdb Resolution: 1.61→56.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.492 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.096 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.335 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→56.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.652 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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