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- PDB-1cm9: CRYSTAL STRUCTURE OF VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II -

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Basic information

Entry
Database: PDB / ID: 1cm9
TitleCRYSTAL STRUCTURE OF VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II
ComponentsPROTEIN (VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II)
KeywordsCHEMOKINE / HERPESVIRUS-8 / KARPOSI'S SARCOMA
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
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsFernandez, E.J. / Lolis, E.
CitationJournal: Biochemistry / Year: 2000
Title: Comparison of the structure of vMIP-II with eotaxin-1, RANTES, and MCP-3 suggests a unique mechanism for CCR3 activation.
Authors: Fernandez, E.J. / Wilken, J. / Thompson, D.A. / Peiper, S.C. / Lolis, E.
History
DepositionMay 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II)
B: PROTEIN (VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II)


Theoretical massNumber of molelcules
Total (without water)16,9262
Polymers16,9262
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-15 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.250, 57.610, 49.560
Angle α, β, γ (deg.)90.00, 130.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-81-

HOH

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Components

#1: Protein PROTEIN (VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II) / VMIP-II


Mass: 8462.800 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NON-BIOLOGICAL SEQUENCE / Source: (natural) Human herpesvirus 8 / Genus: Rhadinovirus / References: UniProt: Q98157
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.3 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: used seeding, Fernandez, E,J., (2000) J.Appl.Crystallogr., 33, 168.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
211 %PEG40001reservoir
311 %2-propanol1reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793, 0.9790, 0.9871
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.9791
30.98711
ReflectionResolution: 2.1→30 Å / Num. obs: 8259 / % possible obs: 92.8 % / Redundancy: 2.5 % / Rsym value: 0.064
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rmerge(I) obs: 0.381

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Processing

Software
NameClassification
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 833 9.4 %RANDOM
Rwork0.24 ---
obs0.24 7859 88.9 %-
Displacement parametersBiso mean: 50.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 22 1064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.311
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 9.4 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.2 Å2

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