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Open data
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Basic information
Entry | Database: PDB / ID: 4zkb | |||||||||
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Title | The chemokine binding protein of orf virus complexed with CCL3 | |||||||||
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![]() | Viral Protein/cytokine / Complex / Orf chemokine binding protein / CCL3 / Viral Protein-cytokine complex | |||||||||
Function / homology | ![]() granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain ...granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / cytoskeleton organization / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / calcium ion transport / chemotaxis / positive regulation of tumor necrosis factor production / MAPK cascade / positive regulation of neuron apoptotic process / cell-cell signaling / kinase activity / cellular response to tumor necrosis factor / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Knapp, K.M. / Nakatani, Y. / Krause, K.L. | |||||||||
![]() | ![]() Title: Structures of Orf Virus Chemokine Binding Protein in Complex with Host Chemokines Reveal Clues to Broad Binding Specificity. Authors: Counago, R.M. / Knapp, K.M. / Nakatani, Y. / Fleming, S.B. / Corbett, M. / Wise, L.M. / Mercer, A.A. / Krause, K.L. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4p5iSC ![]() 4zk9C ![]() 4zkcC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30374.613 Da / Num. of mol.: 1 / Fragment: UNP residues 17-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 8551.468 Da / Num. of mol.: 1 / Fragment: UNP residues 24-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate |
-Data collection
Diffraction | Mean temperature: 93.2 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.44 Å / Num. obs: 13416 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4P5I Resolution: 2.9→47.44 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.837 / SU B: 41.375 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.372 / 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: 78.862 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→47.44 Å
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