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- PDB-1f9s: CRYSTAL STRUCTURE OF PLATELET FACTOR 4 MUTANT 2 -

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Basic information

Entry
Database: PDB / ID: 1f9s
TitleCRYSTAL STRUCTURE OF PLATELET FACTOR 4 MUTANT 2
ComponentsPLATELET FACTOR 4
KeywordsCYTOKINE / 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
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.38 Å
AuthorsYang, J. / Doyle, M. / Faulk, T. / Visentin, G. / Aster, R. / Edwards, B.
CitationJournal: 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
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLATELET FACTOR 4
B: PLATELET FACTOR 4
C: PLATELET FACTOR 4
D: PLATELET FACTOR 4


Theoretical massNumber of molelcules
Total (without water)30,8484
Polymers30,8484
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-32 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.400, 77.480, 42.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer constructed from chain A,B,C and D obeying approximately P222 symmetry

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Components

#1: Protein
PLATELET FACTOR 4 / / PF-4 / ONCOSTATIN / IROPLACT


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 1000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.38→2.47 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.899 / Num. unique all: 506 / % possible all: 47.2

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.288 975 10.5 %RANDOM
Rwork0.228 ---
obs0.228 9318 83.9 %-
all-9318 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.64 Å2 / ksol: 0.258 e/Å3
Displacement parametersBiso mean: 68.1 Å2
Baniso -1Baniso -2Baniso -3
1-18.99 Å20 Å20 Å2
2---26.55 Å20 Å2
3---7.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.39 Å
Luzzati d res low-15 Å
Luzzati sigma a0.56 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.38→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 0 146 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it2.141.5
X-RAY DIFFRACTIONc_mcangle_it3.782
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.752.5
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.443 99 12.9 %
Rwork0.427 667 -
obs--42.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP

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