[English] 日本語
Yorodumi- PDB-5eiv: Crystal structure of complex of osteoclast-associated immunoglobu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eiv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of complex of osteoclast-associated immunoglobulin-like receptor (OSCAR) and a synthetic collagen consensus peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / oscar / collagen / immunoglobulin / triple helix / structural protein | ||||||
Function / homology | Function and homology information collagen receptor activity / osteoclast differentiation / specific granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / tertiary granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.414 Å | ||||||
Authors | Zhou, L. / Blaszczyk, M. / Chirgadze, D. / Bihan, D. / Farndale, R.W. | ||||||
Citation | Journal: Blood / Year: 2016 Title: Structural basis for collagen recognition by the immune receptor OSCAR. Authors: Zhou, L. / Hinerman, J.M. / Blaszczyk, M. / Miller, J.L. / Conrady, D.G. / Barrow, A.D. / Chirgadze, D.Y. / Bihan, D. / Farndale, R.W. / Herr, A.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5eiv.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5eiv.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 5eiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eiv_validation.pdf.gz | 558.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5eiv_full_validation.pdf.gz | 574.5 KB | Display | |
Data in XML | 5eiv_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 5eiv_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/5eiv ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5eiv | HTTPS FTP |
-Related structure data
Related structure data | 5eiqSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein/peptide , 2 types, 9 molecules CDEFGHIJK
#2: Protein/peptide | Mass: 1897.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Protein/peptide | Mass: 665.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
---|
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 22294.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSCAR / Plasmid: pCEP-Pu / Details (production host): C-terminal His tag / Cell line (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: Q8IYS5 #4: Sugar | |
---|
-Non-polymers , 5 types, 329 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: Ammonium Sulphate, Sodium Citate, Glycerol, MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-k,-l / Fraction: 0.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.414→136.585 Å / Num. all: 28164 / Num. obs: 28164 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.149 / Rsym value: 0.127 / Net I/av σ(I): 5.692 / Net I/σ(I): 11 / Num. measured all: 190535 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5eiq Resolution: 2.414→70.584 Å / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 33.37 / Stereochemistry target values: TWIN_LSQ_F
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.44 Å2 / Biso mean: 33.2623 Å2 / Biso min: 18.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.414→70.584 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|