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- PDB-4ffe: The structure of cowpox virus CPXV018 (OMCP) -

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Basic information

Entry
Database: PDB / ID: 4ffe
TitleThe structure of cowpox virus CPXV018 (OMCP)
ComponentsCPXV018 protein
KeywordsVIRAL PROTEIN / Viral immune evasion proteins / structural genomics / NKG2D decoy ligand / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / secreted / NKG2D binding / FcRL5 binding
Function / homologyMHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 2-Layer Sandwich / Alpha Beta / CPXV018 protein
Function and homology information
Biological speciesCowpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsLazear, E. / Peterson, L.W. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Virol. / Year: 2013
Title: Crystal Structure of the Cowpox Virus-Encoded NKG2D Ligand OMCP.
Authors: Lazear, E. / Peterson, L.W. / Nelson, C.A. / Fremont, D.H.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 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 / 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

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Assembly

Deposited unit
X: CPXV018 protein
Y: CPXV018 protein
Z: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)54,1963
Polymers54,1963
Non-polymers00
Water2,954164
1
X: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)18,0651
Polymers18,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)18,0651
Polymers18,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
Z: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)18,0651
Polymers18,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.173, 105.173, 108.657
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CPXV018 protein / OMCP / Orthopox virus MHC class I-like protein


Mass: 18065.223 Da / Num. of mol.: 3 / Fragment: UNP residues 20-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Strain: Brighton Red / Gene: CPXV018 CDS, OMCP / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8QN43
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.9 M ammonium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 4.2.210.979
SYNCHROTRONALS 4.2.220.9792,0.9641
Detector
TypeIDDetectorDate
NOIR-11CCDApr 12, 2008
NOIR-12CCDApr 12, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.96411
ReflectionResolution: 2.25→50 Å / Num. obs: 32729 / % possible obs: 97.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.05 / Χ2: 0.958 / Net I/σ(I): 30.86
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.25-2.335.30.4862.7329330.9588.8
2.33-2.425.40.40430440.96592.6
2.42-2.535.50.29932140.98396.9
2.53-2.676.10.22332701.09399.1
2.67-2.8370.15533331.043100
2.83-3.058.10.10733121.041100
3.05-3.369.30.06333550.931100
3.36-3.859.90.04133440.904100
3.85-4.859.90.03433940.8499.9
4.85-509.60.03135300.949100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→47.334 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.33 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 2005 6.14 %
Rwork0.2137 --
obs0.2161 32644 97.6 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.33 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 138.71 Å2 / Biso mean: 50.1886 Å2 / Biso min: 18.62 Å2
Baniso -1Baniso -2Baniso -3
1-4.6027 Å20 Å2-0 Å2
2--4.6027 Å20 Å2
3----9.2054 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 0 164 3959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023903
X-RAY DIFFRACTIONf_angle_d0.6625271
X-RAY DIFFRACTIONf_chiral_restr0.049549
X-RAY DIFFRACTIONf_plane_restr0.002678
X-RAY DIFFRACTIONf_dihedral_angle_d9.2621422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.30590.38731290.29961954208388
2.3059-2.36820.35061360.2842019215592
2.3682-2.43790.35281370.2612066220393
2.4379-2.51660.30811390.25972138227797
2.5166-2.60650.29231460.25982188233499
2.6065-2.71090.32861390.246722112350100
2.7109-2.83420.29151440.238522272371100
2.8342-2.98370.2741440.235622352379100
2.9837-3.17050.28681480.23122272375100
3.1705-3.41530.25241450.21722292374100
3.4153-3.75890.25291470.198322462393100
3.7589-4.30250.1961440.17612236238099
4.3025-5.41940.211530.180222742427100
5.4194-47.34490.22211540.21123892543100

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