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- PDB-2fj2: Crystal Structure of Viral Macrophage Inflammatory Protein-II -

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Basic information

Entry
Database: PDB / ID: 2fj2
TitleCrystal Structure of Viral Macrophage Inflammatory Protein-II
ComponentsViral macrophage inflammatory protein-II
KeywordsCHEMOKINE / herpesvirus / anti-HIV
Function / homology
Function and homology information


CXCR chemokine receptor binding / chemokine activity / immune response / protein-containing complex / extracellular space
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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
Viral macrophage inflammatory protein 2
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, Y. / Liu, D. / Cao, R. / Kumar, S. / Dong, C.Z. / wilson, S.R. / Gao, Y.G. / Huang, Z.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of chemically synthesized vMIP-II.
Authors: Li, Y. / Liu, D. / Cao, R. / Kumar, S. / Dong, C. / An, J. / Wilson, S.R. / Gao, Y.G. / Huang, Z.
History
DepositionDec 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viral macrophage inflammatory protein-II
B: Viral macrophage inflammatory protein-II
C: Viral macrophage inflammatory protein-II
D: Viral macrophage inflammatory protein-II


Theoretical massNumber of molelcules
Total (without water)32,5714
Polymers32,5714
Non-polymers00
Water1,78399
1
A: Viral macrophage inflammatory protein-II
B: Viral macrophage inflammatory protein-II


Theoretical massNumber of molelcules
Total (without water)16,2852
Polymers16,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13 kcal/mol
Surface area8010 Å2
MethodPISA
2
C: Viral macrophage inflammatory protein-II
D: Viral macrophage inflammatory protein-II


Theoretical massNumber of molelcules
Total (without water)16,2852
Polymers16,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.650, 65.770, 45.620
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Viral macrophage inflammatory protein-II / vMIP-II / vMIP- 1B


Mass: 8142.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: sequence occurs in Kaposi's sarcoma herpes virus-8 / References: UniProt: Q98157
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 100mM Sodium Citrate, 11% PEG 4000, 11% 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10149 / % possible obs: 84.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.3→2.38 Å / % possible all: 90.9

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Phasing

Phasing MRRfactor: 0.514 / Cor.coef. Fo:Fc: 0.405
Highest resolutionLowest resolution
Rotation3 Å29.3 Å
Translation3 Å29.3 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
SHELXrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CM9

1cm9


Resolution: 2.3→10 Å / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.301 456 RANDOM
all0.257 10419 -
obs0.248 --
Displacement parametersBiso mean: 35.332 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 0 99 2183

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