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- PDB-1mkf: VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68 -

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Basic information

Entry
Database: PDB / ID: 1mkf
TitleVIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68
ComponentsM3
KeywordsIMMUNE SYSTEM / HERPESVIRUS / VIRAL IMMUNE EVASION / CHEMOKINE BINDING PROTEIN / DECOY RECEPTOR / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Immunoglobulin-like - #1330 / Chemokine-binding protein M3-like / Chemokine-binding M3, viral / Chemokine-binding M3, subdomain 1, viral / Chemokine-binding M3, subdomain 2, viral / Chemokine-binding M3 superfamily / M3 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsAlexander, J.M. / Fremont, D.H. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor
Authors: Alexander, J.M. / Nelson, C.A. / Van Berkel, V. / Lau, E.K. / Studts, J.M. / Brett, T.J. / Speck, S.H. / Handel, T.M. / Virgin, H.W. / Fremont, D.H.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: M3
B: M3


Theoretical massNumber of molelcules
Total (without water)83,6522
Polymers83,6522
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-22 kcal/mol
Surface area31980 Å2
MethodPISA
2
A: M3
B: M3

A: M3
B: M3


Theoretical massNumber of molelcules
Total (without water)167,3054
Polymers167,3054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area9720 Å2
ΔGint-56 kcal/mol
Surface area60590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.900, 67.300, 93.900
Angle α, β, γ (deg.)90.00, 120.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein M3


Mass: 41826.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: M3 / Plasmid: pFB-1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O41925
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 18% PEG4000, 100MM CACL2, 100MM IMIDAZOLE/MALIC ACID PH 5.1, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113-15 mg/mlprotein1drop
218 %PEG40001reservoir
3100 mM1reservoirCaCl2
4100 mMimidazole malic acid1reservoirpH5.1

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 43484 / Num. obs: 43484 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 40.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.346 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Redundancy: 3.1 % / Num. measured all: 133215 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 97 % / Rmerge(I) obs: 0.346

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNSrefinement
DMphasing
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 25464.2 / Data cutoff high rms absF: 25464.2 / 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
Rfree0.273 2056 5 %RANDOM
Rwork0.228 ---
all-41033 --
obs-41033 92.4 %-
Solvent computationBsol: 57.7995 Å2 / ksol: 0.341932 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.05 Å20 Å21.43 Å2
2---0.69 Å20 Å2
3---8.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-6 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 0 332 6038
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d26
X-RAY DIFFRACTIONo_improper_angle_d0.79
X-RAY DIFFRACTIONo_mcbond_it1.681.5
X-RAY DIFFRACTIONo_mcangle_it2.842
X-RAY DIFFRACTIONo_scbond_it2.192
X-RAY DIFFRACTIONo_scangle_it3.322.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.364 234 5.1 %
Rwork0.323 4314 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 2506
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg26
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.79
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å

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