+Open data
-Basic information
Entry | Database: PDB / ID: 4bfg | ||||||
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Title | Structure of the extracellular portion of mouse CD200R | ||||||
Components | CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 1 | ||||||
Keywords | IMMUNE SYSTEM / PAIRED RECEPTOR / IG DOMAINS / VIRAL MIMICRY / LEUKAEMIA | ||||||
Function / homology | Function and homology information negative regulation of T cell migration / negative regulation of macrophage migration / protein binding involved in heterotypic cell-cell adhesion / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / negative regulation of interleukin-6 production / signaling receptor activity / receptor complex / external side of plasma membrane ...negative regulation of T cell migration / negative regulation of macrophage migration / protein binding involved in heterotypic cell-cell adhesion / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / negative regulation of interleukin-6 production / signaling receptor activity / receptor complex / external side of plasma membrane / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Hatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structures of Cd200/Cd200 Receptor Family and Implications for Topology, Regulation, and Evolution Authors: Hatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bfg.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bfg.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfg ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfg | HTTPS FTP |
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-Related structure data
Related structure data | 4bfeSC 4bfiC 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
-Protein / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 23586.258 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q9ES57 |
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#2: Sugar |
-Non-polymers , 4 types, 152 molecules
#3: Chemical | #4: Chemical | ChemComp-AZI / | #5: Chemical | ChemComp-CYS / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | NUMBERING IN THE PDB IS BASED ON THE START OF THE MATURE SEQUENCE, AS DETERMINED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 4 Details: 15% PEG4000, 0.1M SODIUM ACETATE, 0.2M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→38.84 Å / Num. obs: 15423 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 34.49 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BFE Resolution: 2.08→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9204 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.159
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Displacement parameters | Biso mean: 39.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.22 Å / Total num. of bins used: 8
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