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- PDB-4od8: Crystal structure of the vaccinia virus DNA polymerase holoenzyme... -

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Basic information

Entry
Database: PDB / ID: 4od8
TitleCrystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminus
Components
  • DNA polymerase processivity factor component A20
  • Uracil-DNA glycosylase
KeywordsHYDROLASE/REPLICATION / DNA polymerase processivity factor / DNA binding / DNA polymerase binding / HYDROLASE-REPLICATION complex
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, 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 glycosylase / DNA polymerase processivity factor component OPG148
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsContesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Burmeister, W.P. / Iseni, F.
CitationJournal: Plos Pathog. / Year: 2014
Title: Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit d4 in complex with the a20 N-terminal domain.
Authors: Contesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Betzi, S. / Morelli, X. / Burmeister, W.P. / Iseni, F.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)65,77512
Polymers65,0144
Non-polymers7618
Water6,143341
1
B: Uracil-DNA glycosylase
D: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8876
Polymers32,5072
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-65 kcal/mol
Surface area12940 Å2
MethodPISA
2
A: Uracil-DNA glycosylase
C: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8876
Polymers32,5072
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-61 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.620, 92.620, 145.860
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: 26729.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Copenhagen / Gene: D4R, UNG / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P20536, uracil-DNA glycosylase
#2: Protein DNA polymerase processivity factor component A20


Mass: 5777.560 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-50 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Copenhagen / Gene: A20R / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P20995
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 100 mM bicine, 1.5 M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012 / Details: Si111 monochromator plus toroidal mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→48.62 Å / Num. all: 61990 / Num. obs: 61957 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OWQ

2owq


Resolution: 1.85→46.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.561 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21832 3132 5.1 %RANDOM
Rwork0.17518 ---
obs0.1773 58772 99.86 %-
all-61990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 42 341 4769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024500
X-RAY DIFFRACTIONr_bond_other_d0.0030.024243
X-RAY DIFFRACTIONr_angle_refined_deg2.2011.9666119
X-RAY DIFFRACTIONr_angle_other_deg1.07239804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37624.497189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3315768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0861514
X-RAY DIFFRACTIONr_chiral_restr0.1550.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
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_it1.7881.7372164
X-RAY DIFFRACTIONr_mcbond_other1.7831.7362163
X-RAY DIFFRACTIONr_mcangle_it2.5582.592698
X-RAY DIFFRACTIONr_mcangle_other2.5292.5942699
X-RAY DIFFRACTIONr_scbond_it2.8852.0762336
X-RAY DIFFRACTIONr_scbond_other2.8332.0682336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0962.9793422
X-RAY DIFFRACTIONr_long_range_B_refined6.98915.5645467
X-RAY DIFFRACTIONr_long_range_B_other6.99115.5685468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 233 -
Rwork0.257 4270 -
obs--99.84 %
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)
12.07420.19640.60645.32021.16970.982-0.04840.1868-0.0428-0.50430.11170.1213-0.09760.1339-0.06330.13830.0627-0.05320.0856-0.04220.0317-25.085-30.23519.372
24.45291.3276-1.35328.25040.16273.01410.1798-0.39480.30550.55-0.11660.1282-0.08780.1364-0.06320.14070.0577-0.03430.0934-0.07250.072-26.514-7.46436.594
32.2631-0.4689-0.52911.2290.19361.41970.0221-0.21470.05430.1218-0.0513-0.051-0.09580.10640.02920.09950.02-0.03540.1246-0.04710.099-5.223-34.75446.051
44.7781-0.1464-0.48675.55670.39153.3372-0.10320.1495-0.4848-0.20.158-0.16420.2180.1744-0.05470.05770.0666-0.01540.1631-0.03260.168514.492-52.32434.351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B-2 - 218
2X-RAY DIFFRACTION2D0 - 50
3X-RAY DIFFRACTION3A-1 - 218
4X-RAY DIFFRACTION4C1 - 50

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