+Open data
-Basic information
Entry | Database: PDB / ID: 1f9s | ||||||
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Title | CRYSTAL STRUCTURE OF PLATELET FACTOR 4 MUTANT 2 | ||||||
Components | PLATELET FACTOR 4 | ||||||
Keywords | CYTOKINE / Platelet Factor 4 Mutant 2 | ||||||
Function / homology | Function and homology information CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / defense response to protozoan / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of megakaryocyte differentiation / Common Pathway of Fibrin Clot Formation / negative regulation of angiogenesis / neutrophil chemotaxis / platelet alpha granule lumen / Cell surface interactions at the vascular wall / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / cytokine-mediated signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of cell population proliferation / G alpha (i) signalling events / collagen-containing extracellular matrix / cellular response to lipopolysaccharide / inflammatory response / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.38 Å | ||||||
Authors | Yang, J. / Doyle, M. / Faulk, T. / Visentin, G. / Aster, R. / Edwards, B. | ||||||
Citation | Journal: To be Published Title: Structure Comparison of Two Platelet Factor 4 Mutants with the Wild-type Reveals the Epitopes for the Heparin-induced Thrombocytopenia Antibodies Authors: Yang, J. / Doyle, M. / Faulk, T. / Visentin, G. / Aster, R. / Edwards, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f9s.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f9s.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f9s ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f9s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer constructed from chain A,B,C and D obeying approximately P222 symmetry |
-Components
#1: Protein | Mass: 7712.078 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P02776 #2: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 1000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. all: 10165 / Num. obs: 10165 / % possible obs: 90.9 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.899 / Num. unique all: 506 / % possible all: 47.2 |
-Processing
Software |
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Refinement | Resolution: 2.38→15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 407005.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.64 Å2 / ksol: 0.258 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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