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- PDB-5jks: vaccinia virus D4 R167A mutant /A20(1-50) -

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Basic information

Entry
Database: PDB / ID: 5jks
Titlevaccinia virus D4 R167A mutant /A20(1-50)
Components
  • DNA polymerase processivity factor component A20
  • Uracil-DNA glycosylase
KeywordsHYDROLASE/REPLICATION / DNA POLYMERASE PROCESSIVITY FACTOR / DNA BINDING / DNA POLYMERASE BINDING / HYDROLASE-REPLICATION COMPLEX / hydrolase
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / viral DNA genome replication / DNA replication / DNA repair / DNA binding
Similarity search - Function
Helix Hairpins - #1880 / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / Helix Hairpins / Helix non-globular ...Helix Hairpins - #1880 / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / Helix Hairpins / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / DNA polymerase processivity factor component OPG148
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsContesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Burmeister, W.P. / Peyrefitte, C.N. / Iseni, F.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research Agencyanr--13-bsv8-0014 France
German Research Foundation France
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structural analysis of point mutations at the Vaccinia virus A20/D4 interface.
Authors: Contesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Burmeister, W.P. / Peyrefitte, C.N. / Iseni, F.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uracil-DNA glycosylase
D: DNA polymerase processivity factor component A20
A: Uracil-DNA glycosylase
C: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,47810
Polymers64,9024
Non-polymers5766
Water45025
1
B: Uracil-DNA glycosylase
D: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8356
Polymers32,4512
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-84 kcal/mol
Surface area12920 Å2
MethodPISA
2
A: Uracil-DNA glycosylase
C: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6434
Polymers32,4512
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-43 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.980, 92.980, 145.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 26643.371 Da / Num. of mol.: 2 / Mutation: R167A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: UNG, D4R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20536, uracil-DNA glycosylase
#2: Protein DNA polymerase processivity factor component A20


Mass: 5807.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: N-TERMINAL RESIDUES 1-50 / Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: A20R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20995
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1M bicine pH 7.8, 1.6M ammonium sulphate

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.79→28.84 Å / Num. obs: 18696 / % possible obs: 99.6 % / Redundancy: 9.7 % / Net I/σ(I): 15.4
Reflection shellResolution: 2.79→2.95 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.5 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ODA

4oda


Resolution: 2.79→28.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.655 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 2.261 / ESU R Free: 0.33 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 940 5 %RANDOM
Rwork0.17555 ---
obs0.17844 17725 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.262 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.79→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 30 25 4378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024461
X-RAY DIFFRACTIONr_bond_other_d0.0020.024190
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.966068
X-RAY DIFFRACTIONr_angle_other_deg1.06139679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7075539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15724.505182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95415753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6061512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214909
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02991
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_it4.4365.6612168
X-RAY DIFFRACTIONr_mcbond_other4.4355.662167
X-RAY DIFFRACTIONr_mcangle_it6.6598.4772703
X-RAY DIFFRACTIONr_mcangle_other6.6578.4782704
X-RAY DIFFRACTIONr_scbond_it5.2166.0742293
X-RAY DIFFRACTIONr_scbond_other5.0866.0452269
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0338.8453329
X-RAY DIFFRACTIONr_long_range_B_refined10.52644.8034959
X-RAY DIFFRACTIONr_long_range_B_other10.52644.8114960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.788→2.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 64 -
Rwork0.307 1238 -
obs--96.09 %

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