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- PDB-2grk: Crystal structure of ectromelia virus EVM1 chemokine binding protein -

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Basic information

Entry
Database: PDB / ID: 2grk
TitleCrystal structure of ectromelia virus EVM1 chemokine binding protein
ComponentsEVM001
KeywordsVIRAL PROTEIN / chemokine binding protein / immune system
Function / homologyChemokine-binding protein, viral / Major secreted virus protein / Viral Chemokine Inhibitor; Chain A / Major secreted virus protein, 35kDa / 35kD major secreted virus protein / Poxvirus chemokine inhibitor superfamily / Sandwich / Mainly Beta / 35 kDa chemokine binding protein
Function and homology information
Biological speciesEctromelia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArnold, P.L. / Fremont, D.H.
CitationJournal: J.Virol. / Year: 2006
Title: Structural determinants of chemokine binding by an ectromelia virus-encoded decoy receptor.
Authors: Arnold, P.L. / Fremont, D.H.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / 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: EVM001
B: EVM001


Theoretical massNumber of molelcules
Total (without water)49,3692
Polymers49,3692
Non-polymers00
Water2,198122
1
A: EVM001


Theoretical massNumber of molelcules
Total (without water)24,6851
Polymers24,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EVM001


Theoretical massNumber of molelcules
Total (without water)24,6851
Polymers24,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 55.800, 85.800
Angle α, β, γ (deg.)90.000, 106.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EVM001


Mass: 24684.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Genus: Orthopoxvirus / Strain: Moscow / Gene: EVM001 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JFS0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 2 M ammonium sulfate, 3% ethylene glycol, 0.1 M cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K, pH 6.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2003
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 13573 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.085 / Net I/σ(I): 9.547
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.36 / Rsym value: 0.43 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CQ3

1cq3


Resolution: 2.6→19.88 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 148448.609 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.286 640 5.1 %RANDOM
Rwork0.217 ---
obs0.217 12565 90.3 %-
all-13205 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.26 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å2-3.74 Å2
2---7.65 Å20 Å2
3---9.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 122 3560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.291.5
X-RAY DIFFRACTIONc_mcangle_it3.332
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 95 5.1 %
Rwork0.301 1773 -
obs--80.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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