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Yorodumi- PDB-5cjb: Human Osteoclast Associated Receptor (OSCAR) in complex with a co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cjb | ||||||
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Title | Human Osteoclast Associated Receptor (OSCAR) in complex with a collagen-like peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM/STRUCTURAL PROTEIN / Immunoglobulin-like / Collagen / IMMUNE SYSTEM-STRUCTURAL PROTEIN COMPLEX | ||||||
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: 2.398 Å | ||||||
Authors | Gao, G.F. / Qi, J. / Shi, Y. / Haywood, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis of collagen recognition by human osteoclast-associated receptor and design of osteoclastogenesis inhibitors. Authors: Haywood, J. / Qi, J. / Chen, C.C. / Lu, G. / Liu, Y. / Yan, J. / Shi, Y. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cjb.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cjb.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 5cjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/5cjb ftp://data.pdbj.org/pub/pdb/validation_reports/cj/5cjb | HTTPS FTP |
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-Related structure data
Related structure data | 5cj8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20369.395 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSCAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYS5 | ||
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#2: Protein/peptide | Mass: 2221.340 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% polyvinyl alcohol type II, 0.2M potassium acetate pH 7, 0.1M HEPES NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.398→50 Å / Num. obs: 10822 / % possible obs: 99.7 % / Redundancy: 5.9 % / Net I/σ(I): 18.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CJ8 Resolution: 2.398→37.438 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.398→37.438 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.2318 Å / Origin y: -17.2181 Å / Origin z: -7.3802 Å
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Refinement TLS group | Selection details: all |