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- PDB-8e10: Structure of mouse polymerase beta -

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Basic information

Entry
Database: PDB / ID: 80000000000
TitleStructure of mouse polymerase beta
ComponentsDNA polymerase beta
KeywordsTRANSFERASE / DNA polymerase / DNA binding / base excision repair
Function / homology
Function and homology information


Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / somatic diversification of immunoglobulins / : / synaptonemal complex / Ub-specific processing proteases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / somatic diversification of immunoglobulins / : / synaptonemal complex / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / response to gamma radiation / base-excision repair / spindle microtubule / 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 / microtubule / in utero embryonic development / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-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, beta-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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
MALONIC ACID / DNA polymerase beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsThompson, M.K. / Sharma, N. / Prakash, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: DNA Repair (Amst) / Year: 2023
Title: Pol beta /XRCC1 heterodimerization dictates DNA damage recognition and basal Pol beta protein levels without interfering with mouse viability or fertility.
Authors: Koczor, C.A. / Thompson, M.K. / Sharma, N. / Prakash, A. / Sobol, R.W.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase beta
B: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9464
Polymers57,7382
Non-polymers2082
Water9,980554
1
A: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9732
Polymers28,8691
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9732
Polymers28,8691
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.725, 120.534, 69.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

21A-746-

HOH

31B-501-

HOH

41B-546-

HOH

51B-682-

HOH

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Components

#1: Protein DNA polymerase beta /


Mass: 28868.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Polb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q8K409, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 86.7 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 22.5% w/v PEG3350, 1.5% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 27, 2022 / Details: Incoatec Microfocus Sources 3.0
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.647→34.726 Å / Num. obs: 63779 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.031 / Rrim(I) all: 0.088 / Net I/σ(I): 20.4
Reflection shellResolution: 1.647→1.68 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.031 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3092 / CC1/2: 0.625 / Rpim(I) all: 0.447 / Rrim(I) all: 1.126 / % possible all: 99.9

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Processing

Software
NameVersionClassification
APEX3data collection
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
SAINTV8.40Bdata reduction
Aimless0.7.8data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZQY

1zqy


Resolution: 1.65→34.52 Å / SU ML: 0.1672 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2142 6525 10.24 %
Rwork0.1734 57183 -
obs0.1775 63706 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.41 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 14 554 4440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054092
X-RAY DIFFRACTIONf_angle_d1.05215548
X-RAY DIFFRACTIONf_chiral_restr0.0687603
X-RAY DIFFRACTIONf_plane_restr0.0103735
X-RAY DIFFRACTIONf_dihedral_angle_d13.42771581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.27542170.24481881X-RAY DIFFRACTION99.9
1.67-1.690.27862340.22611852X-RAY DIFFRACTION99.95
1.69-1.710.28862080.22181872X-RAY DIFFRACTION99.95
1.71-1.730.23952200.21461907X-RAY DIFFRACTION99.95
1.73-1.750.2772130.21431849X-RAY DIFFRACTION100
1.75-1.780.25752210.20311877X-RAY DIFFRACTION100
1.78-1.80.25921980.20251902X-RAY DIFFRACTION100
1.8-1.830.26192180.2141894X-RAY DIFFRACTION100
1.83-1.860.2662290.19861879X-RAY DIFFRACTION100
1.86-1.890.24392030.18651890X-RAY DIFFRACTION100
1.89-1.920.22472090.17651887X-RAY DIFFRACTION100
1.92-1.960.22832030.18431905X-RAY DIFFRACTION100
1.96-1.990.23532170.17171883X-RAY DIFFRACTION100
1.99-2.030.222150.17221921X-RAY DIFFRACTION100
2.03-2.080.20222310.161867X-RAY DIFFRACTION100
2.08-2.130.21472280.16281870X-RAY DIFFRACTION100
2.13-2.180.21472150.16441891X-RAY DIFFRACTION100
2.18-2.240.21451960.16611945X-RAY DIFFRACTION100
2.24-2.310.21842070.17181902X-RAY DIFFRACTION99.95
2.31-2.380.22142270.17731883X-RAY DIFFRACTION100
2.38-2.460.21022210.17511910X-RAY DIFFRACTION100
2.46-2.560.24182170.16911895X-RAY DIFFRACTION100
2.56-2.680.23312160.17671911X-RAY DIFFRACTION100
2.68-2.820.2182290.17261918X-RAY DIFFRACTION100
2.82-30.22432300.1751914X-RAY DIFFRACTION100
3-3.230.19022100.17321935X-RAY DIFFRACTION100
3.23-3.550.19932180.15771935X-RAY DIFFRACTION100
3.55-4.070.17512200.14861963X-RAY DIFFRACTION100
4.07-5.120.15652250.13961969X-RAY DIFFRACTION100
5.12-34.520.19872300.18642076X-RAY DIFFRACTION99.14

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