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

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Basic information

Entry
Database: PDB / ID: 4oda
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 / DNA polymerase E9 / 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: 2.2 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)65,83512
Polymers65,0744
Non-polymers7618
Water2,774154
1
B: Uracil-DNA glycosylase
D: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9176
Polymers32,5372
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-63 kcal/mol
Surface area12650 Å2
MethodPISA
2
A: Uracil-DNA glycosylase
C: DNA polymerase processivity factor component A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9176
Polymers32,5372
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-61 kcal/mol
Surface area12720 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
Components on special symmetry positions
IDModelComponents
11B-470-

HOH

21B-471-

HOH

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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: 5807.586 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-50
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.: 154 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
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: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2012 / Details: Si111 monochromator and toroidal mirror
RadiationMonochromator: Si 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.2→54.02 Å / Num. all: 37537 / Num. obs: 37537 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 4 / % 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: 4OD8

4od8


Resolution: 2.2→44.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.489 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1873 5 %RANDOM
Rwork0.19382 ---
obs0.19634 35622 99.57 %-
all-37537 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 42 154 4557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.024509
X-RAY DIFFRACTIONr_bond_other_d0.0020.024248
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9666132
X-RAY DIFFRACTIONr_angle_other_deg1.00939817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76224.497189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00615770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.371514
X-RAY DIFFRACTIONr_chiral_restr0.1290.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02999
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_it1.6862.1712168
X-RAY DIFFRACTIONr_mcbond_other1.6722.1692167
X-RAY DIFFRACTIONr_mcangle_it2.5263.2452703
X-RAY DIFFRACTIONr_mcangle_other2.5243.2642704
X-RAY DIFFRACTIONr_scbond_it2.2632.4172341
X-RAY DIFFRACTIONr_scbond_other2.2122.4222341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.33.543430
X-RAY DIFFRACTIONr_long_range_B_refined6.118.1265280
X-RAY DIFFRACTIONr_long_range_B_other6.10118.0345258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 130 -
Rwork0.308 2602 -
obs--99.93 %
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)
11.91820.16880.34326.314-1.60341.1788-0.1337-0.1673-0.01990.1880.31840.02120.0058-0.2028-0.18460.255-0.1321-0.09240.17450.07560.068725.32-30.6284.839
22.8304-0.3944-1.69269.3826-1.29213.8450.19210.27230.2336-0.8219-0.0233-0.1383-0.1429-0.2925-0.16880.344-0.1166-0.05210.13230.09010.086126.654-7.565-12.148
33.22810.4974-1.01580.9218-0.22171.8140.0610.2719-0.0913-0.0283-0.13790.0332-0.1293-0.09580.07690.1776-0.0283-0.03540.21210.07410.20575.024-34.872-21.843
44.47471.1229-0.29365.49350.20753.04630.0666-0.0932-0.64620.3051-0.07960.08240.171-0.19780.0130.0898-0.0619-0.0160.24160.07070.3279-14.814-52.21-10.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B-10 - 9999
2X-RAY DIFFRACTION2D-10 - 9999
3X-RAY DIFFRACTION3A-10 - 9999
4X-RAY DIFFRACTION4C-10 - 9999

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