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- PDB-5n2e: Structure of the E9 DNA polymerase from vaccinia virus -

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Basic information

Entry
Database: PDB / ID: 5n2e
TitleStructure of the E9 DNA polymerase from vaccinia virus
ComponentsDNA polymerase
KeywordsTRANSFERASE / Vaccinia virus / DNA polymerase / protein-protein interface / family B polymerase / processivity factor
Function / homology
Function and homology information


viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain ...DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / DNA polymerase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.74 Å
AuthorsTarbouriech, N. / Burmeister, W.P. / Iseni, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency13-BSV8-0014 France
CitationJournal: Nat Commun / Year: 2017
Title: The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.
Authors: Tarbouriech, N. / Ducournau, C. / Hutin, S. / Mas, P.J. / Man, P. / Forest, E. / Hart, D.J. / Peyrefitte, C.N. / Burmeister, W.P. / Iseni, F.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.2May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5508
Polymers117,3871
Non-polymers1,1627
Water3,945219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint19 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.415, 133.415, 230.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase


Mass: 117387.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: POL, E9L / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P20509, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters

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Non-polymers , 5 types, 226 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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

CrystalDescription: long needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 9-11% PEG 3000, 20-25% glycerol, 100 mM MES-NaOH pH 6.25
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.74→46 Å / Num. obs: 63014 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rrim(I) all: 0.077 / Net I/σ(I): 18.2
Reflection shellResolution: 2.74→2.81 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 4369 / Rrim(I) all: 0.728 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.74→115.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.503 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23561 3075 4.9 %RANDOM
Rwork0.18605 ---
obs0.18849 59888 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 2.74→115.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8171 0 71 219 8461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198436
X-RAY DIFFRACTIONr_bond_other_d0.0030.028008
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.97311391
X-RAY DIFFRACTIONr_angle_other_deg1.076318460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66651000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09723.775408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.768151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2251559
X-RAY DIFFRACTIONr_chiral_restr0.1020.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021982
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_it6.1857.1633997
X-RAY DIFFRACTIONr_mcbond_other6.1837.1623996
X-RAY DIFFRACTIONr_mcangle_it9.16710.7314992
X-RAY DIFFRACTIONr_mcangle_other9.16610.7334993
X-RAY DIFFRACTIONr_scbond_it6.6567.6524439
X-RAY DIFFRACTIONr_scbond_other6.6557.6524439
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.93411.2356398
X-RAY DIFFRACTIONr_long_range_B_refined13.56755.6639438
X-RAY DIFFRACTIONr_long_range_B_other13.56855.6649438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 229 -
Rwork0.328 4334 -
obs--99.37 %

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