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- PDB-6a9s: The crystal structure of vaccinia virus A26 (residues 1-397) -

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Basic information

Entry
Database: PDB / ID: 6a9s
TitleThe crystal structure of vaccinia virus A26 (residues 1-397)
ComponentsProtein A26
KeywordsVIRAL PROTEIN / Vaccinia virus / virus entry / acid sensitive
Function / homologyOrthopoxvirus A26L/A30L / Orthopoxvirus A26L/A30L protein / Chordopoxvirus fusion protein/multifunctional envelope protein A27 / Chordopoxvirus multifunctional envelope protein A27 / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / Protein A26
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å
AuthorsWang, H.C. / Ko, T.Z. / Luo, Y.C. / Liao, Y.T. / Chang, W.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)106-2321-B-001 -033 Taiwan
Ministry of Science and Technology (Taiwan)106-2311-B-038 -002 Taiwan
CitationJournal: Plos Pathog. / Year: 2019
Title: Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH.
Authors: Chang, H.W. / Yang, C.H. / Luo, Y.C. / Su, B.G. / Cheng, H.Y. / Tung, S.Y. / Carillo, K.J.D. / Liao, Y.T. / Tzou, D.M. / Wang, H.C. / Chang, W.
History
DepositionJul 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein A26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2889
Polymers46,7911
Non-polymers4978
Water10,034557
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, This protein appears as a monomer in the solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.380, 80.718, 53.812
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein A26


Mass: 46791.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR149, A26L / Production host: Escherichia coli (E. coli) / References: UniProt: P24758
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97907 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.18→20 Å / Num. obs: 114858 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.7
Reflection shellResolution: 1.18→1.22 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10993 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
BUCCANEERmodel building
HKL-2000data scaling
SHELXCDphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.18→20 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.97 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13002 5134 5 %RANDOM
Rwork0.10655 ---
obs0.10773 97534 88.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20.04 Å2
2---0.03 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 32 557 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193063
X-RAY DIFFRACTIONr_bond_other_d0.0010.022912
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9494146
X-RAY DIFFRACTIONr_angle_other_deg0.85636697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05324.387155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17115510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6511514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3811.5911432
X-RAY DIFFRACTIONr_mcbond_other1.3771.5891431
X-RAY DIFFRACTIONr_mcangle_it1.752.3921793
X-RAY DIFFRACTIONr_mcangle_other1.752.3941794
X-RAY DIFFRACTIONr_scbond_it2.4671.9361631
X-RAY DIFFRACTIONr_scbond_other2.4531.9361631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8352.782341
X-RAY DIFFRACTIONr_long_range_B_refined4.76816.5134119
X-RAY DIFFRACTIONr_long_range_B_other4.76816.5184120
X-RAY DIFFRACTIONr_rigid_bond_restr4.03435975
X-RAY DIFFRACTIONr_sphericity_free35.25133
X-RAY DIFFRACTIONr_sphericity_bonded10.6356323
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 155 -
Rwork0.148 3126 -
obs--38.31 %

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