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- PDB-2r99: Crystal structure of cyclophilin ABH-like domain of human peptidy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r99 | |||||||||
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Title | Crystal structure of cyclophilin ABH-like domain of human peptidylprolyl isomerase E isoform 1 | |||||||||
![]() | Peptidyl-prolyl cis-trans isomerase E | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Walker, J.R. / Davis, T. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() Title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. Authors: Davis, T.L. / Walker, J.R. / Campagna-Slater, V. / Finerty, P.J. / Paramanathan, R. / Bernstein, G. / MacKenzie, F. / Tempel, W. / Ouyang, H. / Lee, W.H. / Eisenmesser, E.Z. / Dhe-Paganon, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.5 KB | Display | ![]() |
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PDB format | ![]() | 62 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zkcC ![]() 2eslC ![]() 2gw2C ![]() 2he9C ![]() 2hq6C ![]() 2bitS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18985.666 Da / Num. of mol.: 1 / Fragment: Cyclophilin domain: Residues 131-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 34% PEG 8000, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 12, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.61→40 Å / Num. obs: 22683 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.041 / Net I/σ(I): 34.34 |
Reflection shell | Resolution: 1.61→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6.36 / % possible all: 81.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2BIT Resolution: 1.61→33.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.734 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→33.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.65 Å / Total num. of bins used: 20
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