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- PDB-5v1h: DNA polymerase beta binary complex with 8-oxoG:A at the primer te... -

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Basic information

Entry
Database: PDB / ID: 5v1h
TitleDNA polymerase beta binary complex with 8-oxoG:A at the primer terminus
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / LIGASE/DNA / transferase ligase / DNA / TRANSFERASE-DNA / LIGASE-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family ...DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.946 Å
AuthorsFreudenthal, B.D. / Schaich, M.A. / Whitaker, A.M. / Smith, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Authors: Whitaker, A.M. / Smith, M.R. / Schaich, M.A. / Freudenthal, B.D.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
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
A: DNA polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)47,7484
Polymers47,7484
Non-polymers00
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-14 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.380, 79.240, 54.880
Angle α, β, γ (deg.)90.00, 105.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase beta /


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: DNA chain DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')


Mass: 3117.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM imidazole, 350 mM sodium acetate, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.946→50 Å / Num. obs: 61220 / % possible obs: 100 % / Redundancy: 6.1 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3isb

3isb


Resolution: 1.946→39.62 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2724 6180 10.09 %
Rwork0.2193 --
obs0.2246 61220 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.946→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 635 0 431 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073354
X-RAY DIFFRACTIONf_angle_d0.9234652
X-RAY DIFFRACTIONf_dihedral_angle_d17.2791917
X-RAY DIFFRACTIONf_chiral_restr0.052510
X-RAY DIFFRACTIONf_plane_restr0.006493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9463-1.96840.50191890.4231652X-RAY DIFFRACTION86
1.9684-1.99160.34231910.27531731X-RAY DIFFRACTION91
1.9916-2.01590.29982110.21461836X-RAY DIFFRACTION92
2.0159-2.04140.29862060.22511781X-RAY DIFFRACTION93
2.0414-2.06830.27021980.23091853X-RAY DIFFRACTION94
2.0683-2.09660.32162150.24961831X-RAY DIFFRACTION95
2.0966-2.12650.30742090.25141841X-RAY DIFFRACTION96
2.1265-2.15830.28872000.23581868X-RAY DIFFRACTION96
2.1583-2.1920.30492060.20981909X-RAY DIFFRACTION98
2.192-2.22790.25392070.19191897X-RAY DIFFRACTION98
2.2279-2.26640.26422170.19261967X-RAY DIFFRACTION99
2.2664-2.30760.27522350.19541834X-RAY DIFFRACTION99
2.3076-2.35190.29372480.22051937X-RAY DIFFRACTION99
2.3519-2.39990.35692030.23271944X-RAY DIFFRACTION99
2.3999-2.45210.31431750.25181910X-RAY DIFFRACTION99
2.4521-2.50910.35021670.25161943X-RAY DIFFRACTION98
2.5091-2.57190.32482500.25681844X-RAY DIFFRACTION97
2.5719-2.64140.35822000.29811832X-RAY DIFFRACTION94
2.6414-2.71910.40291950.30221738X-RAY DIFFRACTION89
2.7191-2.80690.37991930.31351675X-RAY DIFFRACTION87
2.8069-2.90720.37581870.32191641X-RAY DIFFRACTION85
2.9072-3.02350.33822110.29731693X-RAY DIFFRACTION88
3.0235-3.16110.27992230.24241805X-RAY DIFFRACTION96
3.1611-3.32760.28462330.2451922X-RAY DIFFRACTION99
3.3276-3.5360.20432080.18551929X-RAY DIFFRACTION99
3.536-3.80880.20331920.16211923X-RAY DIFFRACTION98
3.8088-4.19170.2471940.19261931X-RAY DIFFRACTION96
4.1917-4.79740.20932190.16841754X-RAY DIFFRACTION93
4.7974-6.04080.17842200.16491836X-RAY DIFFRACTION95
6.0408-39.62820.17451780.14941783X-RAY DIFFRACTION92

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