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Yorodumi- PDB-4bfi: Structure of the complex of the extracellular portions of mouse C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bfi | ||||||
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Title | Structure of the complex of the extracellular portions of mouse CD200R and mouse CD200 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / PAIRED RECEPTOR / IG DOMAINS / VIRAL MIMICRY / LEUKAEMIA MIMICRY / LEUKAEMIA | ||||||
Function / homology | Function and homology information negative regulation of T cell migration / negative regulation of macrophage migration / negative regulation of macrophage activation / protein binding involved in heterotypic cell-cell adhesion / cell-cell adhesion mediator activity / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / presynaptic active zone ...negative regulation of T cell migration / negative regulation of macrophage migration / negative regulation of macrophage activation / protein binding involved in heterotypic cell-cell adhesion / cell-cell adhesion mediator activity / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / presynaptic active zone / negative regulation of interleukin-6 production / regulation of immune response / cell-cell adhesion / signaling receptor activity / postsynaptic density / receptor complex / neuron projection / negative regulation of cell population proliferation / external side of plasma membrane / axon / neuronal cell body / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 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 | 4bfi.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bfi.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bfi_validation.pdf.gz | 486.8 KB | Display | wwPDB validaton report |
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Full document | 4bfi_full_validation.pdf.gz | 494.3 KB | Display | |
Data in XML | 4bfi_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4bfi_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfi ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfi | HTTPS FTP |
-Related structure data
Related structure data | 4bfeC 4bfgSC C: citing same article (ref.) S: Starting model for refinement |
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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 / Antibody / Sugars , 3 types, 13 molecules AB
#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: Antibody | Mass: 23718.795 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 31-232 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: O54901 |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 29 molecules
#4: Chemical | ChemComp-EDO / |
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#5: Chemical | ChemComp-CYS / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | NUMBERING IN THE PDB IS BASED ON 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: 4.48 Å3/Da / Density % sol: 73 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.0M IMIDAZOLE PH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.984 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→86.04 Å / Num. obs: 16034 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.22→3.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BFG Resolution: 3.22→86.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.879 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.756 / ESU R Free: 0.378 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.502 Å2
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Refinement step | Cycle: LAST / Resolution: 3.22→86.04 Å
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