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- PDB-4bfi: Structure of the complex of the extracellular portions of mouse C... -
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Open data
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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 | ||||||
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![]() | IMMUNE SYSTEM / PAIRED RECEPTOR / IG DOMAINS / VIRAL MIMICRY / LEUKAEMIA MIMICRY / LEUKAEMIA | ||||||
Function / homology | ![]() positive regulation of arginase activity / positive regulation of protein-glutamine gamma-glutamyltransferase activity / negative regulation of T cell migration / negative regulation of matrix metallopeptidase secretion / negative regulation of macrophage migration / : / negative regulation of macrophage activation / positive regulation of CREB transcription factor activity / protein binding involved in heterotypic cell-cell adhesion / negative regulation of neuroinflammatory response ...positive regulation of arginase activity / positive regulation of protein-glutamine gamma-glutamyltransferase activity / negative regulation of T cell migration / negative regulation of matrix metallopeptidase secretion / negative regulation of macrophage migration / : / negative regulation of macrophage activation / positive regulation of CREB transcription factor activity / protein binding involved in heterotypic cell-cell adhesion / negative regulation of neuroinflammatory response / positive regulation of transforming growth factor beta production / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-6 production / regulation of immune response / cell-cell adhesion / signaling receptor activity / cell body / membrane => GO:0016020 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.8 KB | Display | ![]() |
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Full document | ![]() | 494.3 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bfeC ![]() 4bfgSC 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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Unit cell |
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Components
-Protein / Antibody / Sugars , 3 types, 13 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 29 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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