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Yorodumi- PDB-1plf: THE THREE-DIMENSIONAL STRUCTURE OF BOVINE PLATELET FACTOR 4 AT 3.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1plf | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF BOVINE PLATELET FACTOR 4 AT 3.0 ANGSTROMS RESOLUTION | ||||||
Components | PLATELET FACTOR 4 | ||||||
Keywords | PLATELET FACTOR | ||||||
Function / homology | Function and homology information CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / leukocyte chemotaxis / chemokine activity / negative regulation of megakaryocyte differentiation / neutrophil chemotaxis / negative regulation of angiogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / leukocyte chemotaxis / chemokine activity / negative regulation of megakaryocyte differentiation / neutrophil chemotaxis / negative regulation of angiogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / cytokine-mediated signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell population proliferation / heparin binding / cellular response to lipopolysaccharide / inflammatory response / immune response / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | St Charles, R. / Edwards, B.F.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1989 Title: The three-dimensional structure of bovine platelet factor 4 at 3.0-A resolution. Authors: St Charles, R. / Walz, D.A. / Edwards, B.F. #1: Journal: J.Mol.Biol. / Year: 1984 Title: X-Ray Diffraction Analysis of Crystals of Bovine Platelet Factor 4 Authors: Charles, R.St. / Ciaglowski, R.E. / Walz, D. / Edwards, B.F.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1plf.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1plf.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 1plf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1plf_validation.pdf.gz | 403.6 KB | Display | wwPDB validaton report |
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Full document | 1plf_full_validation.pdf.gz | 417 KB | Display | |
Data in XML | 1plf_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1plf_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/1plf ftp://data.pdbj.org/pub/pdb/validation_reports/pl/1plf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7885.171 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02777 #2: Chemical | ChemComp-TCN / | #3: Water | ChemComp-HOH / | Compound details | THE FIRST THIRTEEN RESIDUES OF THE NATIVE PROTEIN WERE PROTEOLYTICALLY REMOVED WITH PORCINE ...THE FIRST THIRTEEN RESIDUES OF THE NATIVE PROTEIN WERE PROTEOLYTI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.36 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. all: 7080 / Num. measured all: 6901 / Rmerge(I) obs: 0.047 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 2 Details: THERE IS ONE NI(CN)4 (-2) ANION BOUND PER TETRAMER IN THE UNIT CELL. BINDING OF THIS COMPLEX WAS NECESSARY IN ORDER TO PREPARE A CRYSTAL FORM ISOMORPHOUS WITH A SINGLE PT(CN)4 DERIVATIVE ...Details: THERE IS ONE NI(CN)4 (-2) ANION BOUND PER TETRAMER IN THE UNIT CELL. BINDING OF THIS COMPLEX WAS NECESSARY IN ORDER TO PREPARE A CRYSTAL FORM ISOMORPHOUS WITH A SINGLE PT(CN)4 DERIVATIVE USED IN PHASING THE PARENT CRYSTAL DATA.
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 14466 / σ(F): 2 / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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