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- PDB-5cyw: Crystal Structure of Vaccinia Virus C7 -

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Basic information

Entry
Database: PDB / ID: 5cyw
TitleCrystal Structure of Vaccinia Virus C7
ComponentsInterferon antagonist C7
KeywordsVIRAL PROTEIN / host-range / beta-sandwich / poxvirus / vaccinia
Function / homologyPoxvirus C7/F8A / Poxvirus C7/F8A protein / : / Interferon antagonist C7
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKrumm, B.E. / Meng, X. / Li, Y. / Xiang, Y. / Deng, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI079217 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI113539 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for antagonizing a host restriction factor by C7 family of poxvirus host-range proteins.
Authors: Meng, X. / Krumm, B. / Li, Y. / Deng, J. / Xiang, Y.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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
B: Interferon antagonist C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4033
Polymers18,2191
Non-polymers1842
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon antagonist C7
hetero molecules

B: Interferon antagonist C7
hetero molecules

B: Interferon antagonist C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2099
Polymers54,6563
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area3920 Å2
ΔGint-25 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.653, 100.653, 100.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Interferon antagonist C7 / C7L / Host range protein 2


Mass: 18218.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Ankara) / Strain: Ankara / Gene: MVA018L, ACAM3000_MVA_018, C7L / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68598
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 4.66 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 3.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 23258 / Num. obs: 22967 / % possible obs: 98.7 % / Redundancy: 19.9 % / Biso Wilson estimate: 34.09 Å2 / Rsym value: 0.068 / Net I/σ(I): 50.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.8 / % possible all: 86.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→45.013 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 1168 5.09 %
Rwork0.1531 --
obs0.1546 22941 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 12 159 1436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021310
X-RAY DIFFRACTIONf_angle_d1.6561766
X-RAY DIFFRACTIONf_dihedral_angle_d15.014494
X-RAY DIFFRACTIONf_chiral_restr0.11184
X-RAY DIFFRACTIONf_plane_restr0.009221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.09090.26141230.22972437X-RAY DIFFRACTION89
2.0909-2.20120.22891520.18142716X-RAY DIFFRACTION100
2.2012-2.33910.19531460.15652736X-RAY DIFFRACTION100
2.3391-2.51960.2151340.16362739X-RAY DIFFRACTION100
2.5196-2.77320.18411380.15792749X-RAY DIFFRACTION100
2.7732-3.17440.20791550.16462758X-RAY DIFFRACTION100
3.1744-3.9990.14371470.13322778X-RAY DIFFRACTION100
3.999-45.02480.17351730.14512860X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.36491.28370.91224.47840.7893.6316-0.20770.0963-0.31190.2710.1912-0.38770.21560.2076-0.03990.2480.04280.00670.2511-0.02130.24910.6079-23.7597-5.6159
24.25653.24122.12368.81723.90764.4605-0.1586-0.2422-0.02190.4013-0.0304-0.23290.0250.0780.14870.31940.0197-00.31360.00250.29535.6616-18.87210.7796
32.79140.7757-0.26389.12171.4383.3933-0.04970.0724-0.097-0.1385-0.0394-0.24420.1853-0.01480.01120.18890.03330.01010.27290.00870.21916.0754-20.6934-10.4305
41.721-2.6105-1.95516.52582.35522.34180.02270.1577-0.05290.0103-0.14990.5267-0.0041-0.18220.16640.19410.01040.01180.26420.00130.2123-1.938-13.7357-6.2555
51.8156-0.5782-0.47924.68491.14591.87070.04160.1092-0.04280.02810.0153-0.16180.00940.11730.02070.18760.0221-0.00340.26140.00340.2375.1156-14.5052-8.2786
62.50271.0734-1.70991.2061-0.3398.35540.0608-0.4746-0.09090.41230.1681.26950.4192-1.4436-0.06860.476-0.00530.12750.49830.06060.5447-5.2056-24.36082.5292
78.0543.40782.70324.32562.07772.6863-0.186-0.6043-0.0810.64730.1029-0.2670.24310.21030.00340.4090.0826-0.04640.367-0.02410.290511.1822-18.22026.01
86.1324-0.09970.29381.72380.83093.8086-0.11840.35790.10090.020.0894-0.3197-0.11310.5049-0.09020.28130.06160.00280.2859-0.00260.348216.3821-23.2234-6.1593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resseq 3:22)
2X-RAY DIFFRACTION2(chain B and resseq 23:38)
3X-RAY DIFFRACTION3(chain B and resseq 39:56)
4X-RAY DIFFRACTION4(chain B and resseq 57:72)
5X-RAY DIFFRACTION5(chain B and resseq 73:100)
6X-RAY DIFFRACTION6(chain B and resseq 101:110)
7X-RAY DIFFRACTION7(chain B and resseq 111:129)
8X-RAY DIFFRACTION8(chain B and resseq 130:149)

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