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- PDB-1rhp: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLATELET FACTOR 4 -

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Basic information

Entry
Database: PDB / ID: 1rhp
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLATELET FACTOR 4
ComponentsPLATELET FACTOR 4
KeywordsPLATELET FACTOR
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: 2.4 Å
AuthorsChen, L. / Zhang, X.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of recombinant human platelet factor 4.
Authors: Zhang, X. / Chen, L. / Bancroft, D.P. / Lai, C.K. / Maione, T.E.
History
DepositionSep 16, 1994-
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)31,1294
Polymers31,1294
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-40 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.200, 86.200, 43.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PLATELET FACTOR 4 /


Mass: 7782.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02776
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
210 mMsodium acetate1drop
3150 mMsodium chloride1drop
510 mMsodium acetate1reservoir
41reservoirpH is adjusted to 7.9 by NH4OHNH4OH

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. obs: 11037 / % possible obs: 94.4 % / Rmerge(I) obs: 0.0605
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / % possible obs: 81.5 % / Num. unique obs: 1202

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.241 -
obs0.241 11037
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 91 2079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.89

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