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- PDB-4w5x: The structure of Vaccina virus H7 protein displays A Novel Phosph... -

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Basic information

Entry
Database: PDB / ID: 4w5x
TitleThe structure of Vaccina virus H7 protein displays A Novel Phosphoinositide binding fold required for membrane biogenesis
ComponentsLate protein H7
KeywordsVIRAL PROTEIN / protein phosphoinositide / membrane biogenesis / poxvirus / lipid binding
Function / homologyLate protein H7, poxvirus / Late protein H7 / host cell membrane / host cell cytoplasm / membrane / Late protein OPG112
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsKolli, S. / Deng, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081928 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI113539 United States
CitationJournal: J.Virol. / Year: 2015
Title: Structure-function analysis of vaccinia virus h7 protein reveals a novel phosphoinositide binding fold essential for poxvirus replication.
Authors: Kolli, S. / Meng, X. / Wu, X. / Shengjuler, D. / Cameron, C.E. / Xiang, Y. / Deng, J.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Late protein H7
A: Late protein H7


Theoretical massNumber of molelcules
Total (without water)27,7222
Polymers27,7222
Non-polymers00
Water3,027168
1
A: Late protein H7


Theoretical massNumber of molelcules
Total (without water)13,8611
Polymers13,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Late protein H7


Theoretical massNumber of molelcules
Total (without water)13,8611
Polymers13,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.785, 34.207, 67.200
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Late protein H7 / Protein H8


Mass: 13860.971 Da / Num. of mol.: 2 / Fragment: unp residues 1-118 / Mutation: C89S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / Gene: VACWR105, H7R / Production host: Escherichia Coli (E. coli) / Strain (production host): bl21goldDE3 / References: UniProt: P08586
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.8
Details: 0.08M Bis-Tris phosphate/citric acid, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16966 / % possible obs: 97.6 % / Redundancy: 4.6 % / Net I/σ(I): 17
Reflection shellResolution: 2→2.07 Å / % possible all: 87.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.002→39.485 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 1616 9.93 %
Rwork0.1955 --
obs0.2007 16276 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.753 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.8565 Å2-0 Å22.7571 Å2
2---2.3028 Å20 Å2
3----13.5537 Å2
Refinement stepCycle: LAST / Resolution: 2.002→39.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 168 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071933
X-RAY DIFFRACTIONf_angle_d0.9572592
X-RAY DIFFRACTIONf_dihedral_angle_d13.786736
X-RAY DIFFRACTIONf_chiral_restr0.064290
X-RAY DIFFRACTIONf_plane_restr0.003327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0017-2.07330.32151270.21821179X-RAY DIFFRACTION78
2.0733-2.15630.29791520.20281367X-RAY DIFFRACTION87
2.1563-2.25440.2711510.20691385X-RAY DIFFRACTION90
2.2544-2.37320.31581560.20391436X-RAY DIFFRACTION93
2.3732-2.52190.25651630.20981501X-RAY DIFFRACTION96
2.5219-2.71660.29051710.21411512X-RAY DIFFRACTION97
2.7166-2.98990.25891720.22391522X-RAY DIFFRACTION97
2.9899-3.42230.25311700.20861554X-RAY DIFFRACTION98
3.4223-4.31090.21921750.1711570X-RAY DIFFRACTION100
4.3109-39.49280.21790.16751634X-RAY DIFFRACTION99

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