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- PDB-1zkc: Crystal Structure of the cyclophiln_RING domain of human peptidyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zkc | ||||||
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Title | Crystal Structure of the cyclophiln_RING domain of human peptidylprolyl isomerase (cyclophilin)-like 2 isoform b | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase like 2 | ||||||
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Function / homology | ![]() Basigin interactions / ubiquitin-ubiquitin ligase activity / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Walker, J.R. / Davis, T. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / 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 | ![]() | 180.3 KB | Display | ![]() |
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PDB format | ![]() | 142.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2eslC ![]() 2gw2C ![]() 2he9C ![]() 2hq6C ![]() 2r99C ![]() 1iipS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22168.861 Da / Num. of mol.: 2 / Fragment: sequence databank residues 20-197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 49.98 % |
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Crystal grow![]() | Temperature: 298 K / pH: 7.5 Details: 0.8M Potassium Sodium Tartrate tetrahydrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.65→30 Å / Num. obs: 57395 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.86 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.72 / % possible all: 63.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1IIP Resolution: 1.65→25.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.247 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.084 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→25.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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