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- PDB-4yig: vaccinia virus D4/A20(1-50) in complex with dsDNA containing an a... -

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Basic information

Entry
Database: PDB / ID: 4yig
Titlevaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free uracyl
Components
  • DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
  • DNA polymerase processivity factor component A20
  • Uracil-DNA glycosylase
KeywordsHYDROLASE / uracyl DNA glycosylase / DNA complex / 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 / DNA / Uracil-DNA glycosylase / DNA polymerase processivity factor component OPG148
Similarity search - Component
Biological speciesVaccinia virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
Authorstarbouriech, N. / burmeister, W.P. / iseni, F.
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
DepositionMar 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: DNA polymerase processivity factor component A20
C: DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
E: Uracil-DNA glycosylase
F: DNA polymerase processivity factor component A20
G: DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
H: DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
I: Uracil-DNA glycosylase
J: DNA polymerase processivity factor component A20
K: DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
L: DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,79415
Polymers115,45812
Non-polymers3363
Water97354
1
A: Uracil-DNA glycosylase
B: DNA polymerase processivity factor component A20
C: DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5985
Polymers38,4864
Non-polymers1121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Uracil-DNA glycosylase
F: DNA polymerase processivity factor component A20
G: DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
H: DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5985
Polymers38,4864
Non-polymers1121
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Uracil-DNA glycosylase
J: DNA polymerase processivity factor component A20
K: DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')
L: DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5985
Polymers38,4864
Non-polymers1121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.092, 136.092, 161.073
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21G
31K
12D
22H
32L

NCS domain segments:

Component-ID: 1 / Refine code: 6 / Label seq-ID: 1 - 10

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-ID
11DCDCDTDTCC1 - 10
21DCDCDTDTGG1 - 10
31DCDCDTDTKK1 - 10
12DADADGDGDD22 - 31
22DADADGDGHH22 - 31
32DADADGDGLL22 - 31

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.531761, -0.845811, 0.04282), (0.845334, 0.527034, -0.087439), (0.051389, 0.082694, 0.995249)1.13413, 75.95432, -25.52794
3given(-0.613223, -0.789907, 0.002149), (0.783515, -0.60791, 0.128648), (-0.100313, 0.080573, 0.991688)-72.04012, 35.43469, -59.17456
4given(1), (1), (1)
5given(0.544174, -0.835047, 0.081061), (0.838317, 0.537385, -0.091885), (0.033168, 0.117956, 0.992465)1.86461, 75.28272, -27.71732
6given(-0.635708, -0.77113, 0.035109), (0.769264, -0.629081, 0.111759), (-0.064094, 0.098054, 0.993115)-73.71944, 35.64613, -58.07341

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Components

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Protein , 2 types, 6 molecules AEIBFJ

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 26729.486 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (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: 5777.560 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: A20R / Production host: Escherichia coli BL21(de3) (bacteria) / References: UniProt: P20995

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DNA chain , 2 types, 6 molecules CGKDHL

#3: DNA chain DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3')


Mass: 2892.878 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3')


Mass: 3086.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 57 molecules

#5: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.73 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.2M ammonium chloride, 10% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→48.86 Å / Num. obs: 46345 / % possible obs: 99.9 % / Redundancy: 5 % / Rsym value: 0.045 / Net I/σ(I): 19.1
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OD8,1SSP

4od8

1ssp


Resolution: 2.7→48.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.5 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22764 2227 4.8 %RANDOM
Rwork0.17993 ---
obs0.18227 44109 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.761 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.7→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 1188 24 54 7824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0188082
X-RAY DIFFRACTIONr_bond_other_d0.0060.027086
X-RAY DIFFRACTIONr_angle_refined_deg1.821.82411187
X-RAY DIFFRACTIONr_angle_other_deg1.348316404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46824.227291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.443151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2861527
X-RAY DIFFRACTIONr_chiral_restr0.1020.21197
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218103
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021788
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_it5.9437.0743234
X-RAY DIFFRACTIONr_mcbond_other5.9437.0743233
X-RAY DIFFRACTIONr_mcangle_it8.30210.5974032
X-RAY DIFFRACTIONr_mcangle_other8.30110.5974033
X-RAY DIFFRACTIONr_scbond_it6.817.6914848
X-RAY DIFFRACTIONr_scbond_other6.8097.6914849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.70211.3877156
X-RAY DIFFRACTIONr_long_range_B_refined12.00460.3419428
X-RAY DIFFRACTIONr_long_range_B_other12.00460.3459427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C304loose positional0.385
11G304loose positional0.355
11K304loose positional0.375
22D318loose positional0.295
22H318loose positional0.315
22L318loose positional0.455
11C304loose thermal8.9510
11G304loose thermal6.1810
11K304loose thermal13.5310
22D318loose thermal13.0710
22H318loose thermal6.6710
22L318loose thermal15.0510
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 160 -
Rwork0.316 3275 -
obs--100 %

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