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- PDB-3ici: Crystal structure of cyclophilin B in complex with calmegin fragment -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ici | ||||||
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Title | Crystal structure of cyclophilin B in complex with calmegin fragment | ||||||
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![]() | ISOMERASE / protein-protein complex / Endoplasmic reticulum / Glycoprotein / Rotamase / Chaperone / Lectin / Membrane / Phosphoprotein / Transmembrane | ||||||
Function / homology | ![]() : / endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / protein peptidyl-prolyl isomerization ...: / endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / neutrophil chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / bone development / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / melanosome / protein folding / protein stabilization / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kozlov, G. / Gehring, K. | ||||||
![]() | ![]() Title: Structural Basis of Cyclophilin B Binding by the Calnexin/Calreticulin P-domain. Authors: Kozlov, G. / Bastos-Aristizabal, S. / Maattanen, P. / Rosenauer, A. / Zheng, F. / Killikelly, A. / Trempe, J.F. / Thomas, D.Y. / Gehring, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.8 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ichC ![]() 1cynS C: citing same article ( S: Starting model for refinement |
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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: 20735.787 Da / Num. of mol.: 2 / Fragment: UNP residues 34-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 4342.601 Da / Num. of mol.: 1 / Fragment: P-domain fragment: residues 317-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE SEQUENCE OF ENTITY 2 (CHAIN C) CORRESPONDS TO RESIDUES 317-350 OF DOG ...AUTHORS STATE THAT THE SEQUENCE OF ENTITY 2 (CHAIN C) CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22% w/v PEG 8000, 10mM ZnCl2, 0.1M Tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9995 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 38845 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2598 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1CYN Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.316 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.291 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.75 Å / Total num. of bins used: 20
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