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- PDB-4ygm: Vaccinia virus his-D4/A20(1-50) in complex with uracil -

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Basic information

Entry
Database: PDB / ID: 4ygm
TitleVaccinia virus his-D4/A20(1-50) in complex with uracil
Components
  • DNA polymerase processivity factor component A20
  • Uracil-DNA glycosylase
KeywordsHYDROLASE / Uracil DNA glycosidase / virus replication
Function / homology
Function and homology information


uracil-DNA glycosylase / viral DNA genome replication / uracil DNA N-glycosylase activity / DNA replication / DNA repair / DNA binding
Similarity search - Function
Helix Hairpins - #1880 / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like domain superfamily / Helix Hairpins / Helix non-globular ...Helix Hairpins - #1880 / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like domain superfamily / Helix Hairpins / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URACIL / Uracil-DNA glycosylase / DNA polymerase processivity factor component OPG148
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTarbouriech, N. / Iseni, F. / Burmeister, W.P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agencyanr-13-bsv8-0014 France
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.
Authors: Burmeister, W.P. / Tarbouriech, N. / Fender, P. / Contesto-Richefeu, C. / Peyrefitte, C.N. / Iseni, F.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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)65,97113
Polymers65,0744
Non-polymers8979
Water6,810378
1
B: Uracil-DNA glycosylase
D: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0337
Polymers32,5372
Non-polymers4965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Uracil-DNA glycosylase
C: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9376
Polymers32,5372
Non-polymers4004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.786, 92.786, 146.744
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-304-

SO4

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 26729.486 Da / Num. of mol.: 2
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 / Fragment: UNP residues 1-50
Source method: isolated from a genetically manipulated source
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.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 0.1M bicine, 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→81 Å / Num. obs: 63182 / % possible obs: 96.4 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.2
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.6 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OD8

4od8


Resolution: 1.85→80.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.546 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22248 2992 5 %RANDOM
Rwork0.19067 ---
obs0.19229 57089 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.85→80.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 51 378 4795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024523
X-RAY DIFFRACTIONr_bond_other_d0.0020.024268
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9656146
X-RAY DIFFRACTIONr_angle_other_deg1.02339855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0025535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87724.197193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18215781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9661518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021020
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_it1.2722.2422152
X-RAY DIFFRACTIONr_mcbond_other1.2682.2412151
X-RAY DIFFRACTIONr_mcangle_it2.0753.3522683
X-RAY DIFFRACTIONr_mcangle_other2.0753.3522684
X-RAY DIFFRACTIONr_scbond_it1.6812.5232371
X-RAY DIFFRACTIONr_scbond_other1.682.5232372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7673.6843464
X-RAY DIFFRACTIONr_long_range_B_refined5.48919.3315483
X-RAY DIFFRACTIONr_long_range_B_other5.40818.85319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 196 -
Rwork0.358 4161 -
obs--94.51 %
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)
10.51510.05990.24212.023-0.33010.19-0.0271-0.0843-0.05040.0690.0677-0.1075-0.004-0.0757-0.04060.0923-0.0563-0.05670.06890.06240.094825.229-29.9534.97
20.16630.2385-0.60244.8338-1.38532.32520.06230.02710.1053-0.47570.339-0.3658-0.0762-0.213-0.40120.181-0.10950.02310.10210.05980.202926.394-7.555-12.401
31.21030.197-0.29570.0861-0.09880.64030.0060.12020.01240.0171-0.044-0.0094-0.0276-0.07840.0380.0159-0.0199-0.02460.11240.030.10084.886-34.762-21.82
42.05330.8837-0.74043.754-0.85570.6899-0.08590.065-0.30640.13450.12450.1247-0.1171-0.1532-0.03860.0690.01660.03570.10330.07280.1803-14.473-52.124-10.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 218
2X-RAY DIFFRACTION2D1 - 50
3X-RAY DIFFRACTION3A-1 - 218
4X-RAY DIFFRACTION4C0 - 50

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