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- PDB-5ej0: The vaccinia virus H3 envelope protein, a major target of neutral... -

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Basic information

Entry
Database: PDB / ID: 5ej0
TitleThe vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose
ComponentsEnvelope protein H3
KeywordsVIRAL PROTEIN / H3 / vaccinia virus / poxvirus / glycosyl transferase
Function / homology
Function and homology information


viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Poxvirus P35 / Poxvirus P35 protein
Similarity search - Domain/homology
2-AMINO-ETHANETHIOL / ETHANOL / METHANOL / 1,3-PROPANDIOL / N-PROPANOL / Envelope protein OPG108
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSingh, K. / Gittis, A.G. / Gitti, R.K. / Ostazesky, S.A. / Su, H.P. / Garboczi, D.N.
CitationJournal: J.Virol. / Year: 2016
Title: The Vaccinia Virus H3 Envelope Protein, a Major Target of Neutralizing Antibodies, Exhibits a Glycosyltransferase Fold and Binds UDP-Glucose.
Authors: Singh, K. / Gittis, A.G. / Gitti, R.K. / Ostazeski, S.A. / Su, H.P. / Garboczi, D.N.
History
DepositionOct 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,10626
Polymers27,4861
Non-polymers1,61925
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.360, 54.790, 111.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Envelope protein H3 / Ag35 / Virion envelope protein p35


Mass: 27486.207 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: VACWR101, H3L / Plasmid: pNAN / Production host: Escherichia coli (E. coli) / References: UniProt: P07240

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Non-polymers , 10 types, 116 molecules

#2: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NS
#3: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#9: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4O
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS HAVE INDICATED THAT THE SEQUENCE IN THE UNPROT ENTRY P07240 IS INCORRECT

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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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM citric acid, 10-20% PEG 6000, 5% 1,3-propanediol and mixture of low molecular mass alcohols

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2005
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→49.22 Å / Num. obs: 21213 / % possible obs: 99.81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.79 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.54

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→49.216 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1668 7.86 %
Rwork0.1973 19545 -
obs0.2007 21213 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.01 Å2 / Biso mean: 33.3324 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 1.9→49.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 105 91 1840
Biso mean--41.1 38.37 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081765
X-RAY DIFFRACTIONf_angle_d1.0892340
X-RAY DIFFRACTIONf_chiral_restr0.04264
X-RAY DIFFRACTIONf_plane_restr0.005291
X-RAY DIFFRACTIONf_dihedral_angle_d12.369611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.9560.31161560.287115901746100
1.956-2.01910.32771530.260815851738100
2.0191-2.09130.29541250.222316021727100
2.0913-2.1750.25541270.215116011728100
2.175-2.2740.22851490.201515911740100
2.274-2.39390.22291220.19416541776100
2.3939-2.54390.24921150.196516241739100
2.5439-2.74030.22921390.209916361775100
2.7403-3.0160.24061390.201816321771100
3.016-3.45240.26781490.18716211770100
3.4524-4.34920.20121430.165516601803100
4.3492-49.23210.22741510.19841749190099

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