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- PDB-3vop: Structure of Vaccinia virus A27 -

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Basic information

Entry
Database: PDB / ID: 3vop
TitleStructure of Vaccinia virus A27
ComponentsProtein A27
KeywordsVIRAL PROTEIN / Vaccinia virus / virus fusion protein / virus envelope protein / coiled-coil protein
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope
Similarity search - Function
Chordopoxvirus fusion protein/multifunctional envelope protein A27 / Chordopoxvirus multifunctional envelope protein A27 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein OPG154
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsChang, T.H. / Ko, T.P. / Hsieh, F.L. / Wang, A.H.J.
CitationJournal: Plos Pathog. / Year: 2013
Title: Crystal structure of vaccinia viral A27 protein reveals a novel structure critical for its function and complex formation with A26 protein.
Authors: Chang, T.H. / Chang, S.J. / Hsieh, F.L. / Ko, T.P. / Lin, C.T. / Ho, M.R. / Wang, I. / Hsu, S.T. / Guo, R.T. / Chang, W. / Wang, A.H.
History
DepositionJan 31, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 18, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein A27
B: Protein A27
C: Protein A27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,24912
Polymers22,2943
Non-polymers9559
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-26 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.190, 79.190, 90.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein A27


Mass: 7431.390 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 21-84 / Mutation: C51A, C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / Gene: A27, A27L, VACWR150 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11258
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.23 % / Mosaicity: 0.703 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M phosphate-citrate, pH 4.5, 0.2M NaCl, 45-50% PEG 200, vapor diffusion, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211
SYNCHROTRONNSRRC BL13B121.25516, 1.25450
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 13, 2007
ADSC QUANTUM 3152CCDJul 13, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontally Focusing Single Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Horizontally Focusing Single Crystal MonochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.255161
31.25451
ReflectionRedundancy: 18.1 % / Av σ(I) over netI: 46.18 / Number: 163881 / Rmerge(I) obs: 0.077 / Χ2: 1.16 / D res high: 2.62 Å / D res low: 30 Å / Num. obs: 9074 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.633099.210.0731.21116
4.485.6310010.0381.09517.4
3.914.4899.910.0341.17418
3.553.9110010.0491.28918.2
3.33.5510010.0861.27718.5
3.113.310010.1651.17818.5
2.953.1110010.2181.10918.6
2.822.9510010.2851.0818.8
2.712.8210010.4511.09618.5
2.622.7110010.6431.09218.5
ReflectionResolution: 2.2→30 Å / Num. all: 15108 / Num. obs: 15074 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.295 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.289.50.5514691.5791,2100
2.28-2.379.60.42514711.5361,2100
2.37-2.489.60.30714961.5181,2100
2.48-2.619.50.22614861.4851,2100
2.61-2.779.50.14714951.251,2100
2.77-2.999.50.08914941.181,2100
2.99-3.299.50.06515201.0361,2100
3.29-3.769.40.03515281.0971,299.7
3.76-4.739.10.02615161.1481,298.3
4.73-308.30.02415991.1131,295.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.779 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 760 5 %RANDOM
Rwork0.2093 ---
obs0.2123 14299 99.33 %-
all-15074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.28 Å2 / Biso mean: 56.506 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 63 130 1229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221093
X-RAY DIFFRACTIONr_angle_refined_deg1.6522.0351432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4825.78957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.52815235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.181159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02747
X-RAY DIFFRACTIONr_mcbond_it0.9331.5615
X-RAY DIFFRACTIONr_mcangle_it1.80421002
X-RAY DIFFRACTIONr_scbond_it3.0893478
X-RAY DIFFRACTIONr_scangle_it5.4654.5430
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 66 -
Rwork0.214 1022 -
all-1088 -
obs-1469 100 %
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)
18.4859-10.1235-2.559817.28674.45411.3795-0.1602-0.44921.17-0.0190.495-0.88-0.26010.1048-0.33480.19030.06370.00590.1647-0.07610.3067-3.50752.6522.286
27.9812-11.6619-1.008524.47932.60542.25480.30210.12330.1397-0.869-0.10860.1398-0.2526-0.4276-0.19340.06620.0785-0.0110.24360.02490.0716-9.33246.56718.677
314.4098-16.95486.373721.1182-8.76853.4452-0.0177-0.1772-0.1736-0.1692-0.0357-0.05690.1650.06790.05340.20220.1106-0.020.1241-0.03420.1343-25.32465.52924.797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 64
2X-RAY DIFFRACTION2B25 - 64
3X-RAY DIFFRACTION3C22 - 64

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