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- PDB-1cq3: STRUCTURE OF A SOLUBLE SECRETED CHEMOKINE INHIBITOR, VCCI, FROM C... -

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Basic information

Entry
Database: PDB / ID: 1cq3
TitleSTRUCTURE OF A SOLUBLE SECRETED CHEMOKINE INHIBITOR, VCCI, FROM COWPOX VIRUS
ComponentsVIRAL CHEMOKINE INHIBITOR
KeywordsCYTOKINE / BETA SANDWICH / CHEMOKINE
Function / homology
Function and homology information


Chemokine-binding protein, viral / Major secreted virus protein / Viral Chemokine Inhibitor; Chain A / Major secreted virus protein, 35kDa / Poxvirus chemokine inhibitor superfamily / Viral chemokine binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Sandwich / Mainly Beta
Similarity search - Domain/homology
D1L protein / VCCI or CPXV003 protein
Similarity search - Component
Biological speciesCowpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsCarfi, A. / Smith, C.A. / Smolak, P.J. / McGrew, J. / Wiley, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of a soluble secreted chemokine inhibitor vCCI (p35) from cowpox virus.
Authors: Carfi, A. / Smith, C.A. / Smolak, P.J. / McGrew, J. / Wiley, D.C.
History
DepositionAug 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIRAL CHEMOKINE INHIBITOR
B: VIRAL CHEMOKINE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)50,7662
Polymers50,7662
Non-polymers00
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.699, 64.423, 245.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

21A-319-

HOH

31A-381-

HOH

41B-367-

HOH

51B-395-

HOH

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Components

#1: Protein VIRAL CHEMOKINE INHIBITOR


Mass: 25383.037 Da / Num. of mol.: 2 / Fragment: NATIVE PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O73568, UniProt: Q85307*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% (w/v) PEG8K,10% Glycerol, 50 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 12 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMTris-HCl1drop
24 mg/mlprotein1drop
320-22 %(v/v)PEG80001reservoir
410 %(w/v)glycerol1reservoir
525 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9188
DetectorType: OTHER / Detector: CCD / Date: May 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 40519 / % possible obs: 86.7 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→20 Å / Redundancy: 3 % / Rmerge(I) obs: 0.157 / % possible all: 52.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementResolution: 1.85→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2035 -RANDOM
Rwork0.213 ---
obs0.213 40117 87.5 %-
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 0 466 3840
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_deg1.4
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
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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