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- PDB-8e11: Structure of mouse DNA polymerase Beta (PolB) mutant -

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Basic information

Entry
Database: PDB / ID: 800000000000
TitleStructure of mouse DNA polymerase Beta (PolB) mutant
ComponentsDNA polymerase beta
KeywordsTRANSFERASE / DNA Polymerase / Base Excision Repair / DNA binding
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 / 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 / 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 / 5'-deoxyribose-5-phosphate lyase activity / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / base-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / in utero embryonic development / microtubule / response to ethanol / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / metal ion binding / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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 family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / 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
ACETATE ION / MALONIC ACID / DNA polymerase beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSharma, N. / Thompson, M.K. / 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)58,2686
Polymers57,9422
Non-polymers3264
Water7,458414
1
A: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1343
Polymers28,9711
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1343
Polymers28,9711
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.372, 39.898, 93.804
Angle α, β, γ (deg.)90.000, 91.710, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

21B-667-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 93 through 103 or resid 105...
d_2ens_1(chain "B" and (resid 93 through 103 or resid 105...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRVALA1 - 11
d_12ens_1GLYLEUA13 - 64
d_13ens_1METSERA66 - 79
d_14ens_1TYRTHRA81 - 109
d_15ens_1GLUSERA111 - 113
d_16ens_1PROLEUA116 - 136
d_17ens_1LYSMETA138 - 186
d_18ens_1ALAGLUA188 - 239
d_21ens_1THRVALB4 - 14
d_22ens_1GLYLEUB16 - 67
d_23ens_1METSERB69 - 82
d_24ens_1TYRTHRB84 - 112
d_25ens_1GLULEUB114 - 137
d_26ens_1LYSMETB139 - 187
d_27ens_1ALAGLUB189 - 240

NCS oper: (Code: givenMatrix: (-0.995594200125, -0.0123501363887, 0.0929497864854), (-0.0126180468619, 0.99991775521, -0.0022951490946), (-0.0929137964454, -0.00345788188868, -0.995668152289)Vector: - ...NCS oper: (Code: given
Matrix: (-0.995594200125, -0.0123501363887, 0.0929497864854), (-0.0126180468619, 0.99991775521, -0.0022951490946), (-0.0929137964454, -0.00345788188868, -0.995668152289)
Vector: -5.85288491178, -0.20007688599, 46.5335719636)

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Components

#1: Protein DNA polymerase beta


Mass: 28970.848 Da / Num. of mol.: 2 / Mutation: L301R, V303R
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 27.5% 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 28, 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: 1.8→31.25 Å / Num. obs: 55670 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.031 / Rrim(I) all: 0.09 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3275 / CC1/2: 0.681 / Rpim(I) all: 0.515 / Rrim(I) all: 1.207 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
PDB-REDOrefinement
SAINTB8.40Bdata reduction
Aimless0.7.8data scaling
PHASER2.8.3phasing
APEX3data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zqy

1zqy


Resolution: 1.8→30.92 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 5656 10.16 %
Rwork0.1923 49994 -
obs0.1963 55650 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.37 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 22 414 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514003
X-RAY DIFFRACTIONf_angle_d0.72035400
X-RAY DIFFRACTIONf_chiral_restr0.0507579
X-RAY DIFFRACTIONf_plane_restr0.0067715
X-RAY DIFFRACTIONf_dihedral_angle_d13.00091541
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.559290484052 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.29391710.26881671X-RAY DIFFRACTION99.62
1.82-1.840.29641770.26871647X-RAY DIFFRACTION100
1.84-1.860.31582010.25731618X-RAY DIFFRACTION99.78
1.86-1.890.29881850.23881694X-RAY DIFFRACTION100
1.89-1.910.29781790.23061643X-RAY DIFFRACTION100
1.91-1.940.3021890.21991616X-RAY DIFFRACTION100
1.94-1.970.2411950.21131677X-RAY DIFFRACTION100
1.97-20.25621880.21221672X-RAY DIFFRACTION100
2-2.030.25961700.21281629X-RAY DIFFRACTION100
2.03-2.060.2721750.20841672X-RAY DIFFRACTION100
2.06-2.10.26221790.2031657X-RAY DIFFRACTION100
2.1-2.130.27111930.19421672X-RAY DIFFRACTION100
2.13-2.180.22921910.18621639X-RAY DIFFRACTION100
2.18-2.220.22271900.19231672X-RAY DIFFRACTION100
2.22-2.270.24961580.19561663X-RAY DIFFRACTION99.95
2.27-2.320.2691410.19241722X-RAY DIFFRACTION100
2.32-2.380.23161850.2031649X-RAY DIFFRACTION99.95
2.38-2.440.26332050.18911642X-RAY DIFFRACTION100
2.44-2.510.23181870.19341683X-RAY DIFFRACTION100
2.51-2.60.24441750.19391657X-RAY DIFFRACTION100
2.6-2.690.252270.19641651X-RAY DIFFRACTION100
2.69-2.80.23291980.20191630X-RAY DIFFRACTION100
2.8-2.920.23021630.19311700X-RAY DIFFRACTION100
2.92-3.080.24062210.20371678X-RAY DIFFRACTION100
3.08-3.270.2422140.20511617X-RAY DIFFRACTION100
3.27-3.520.21071900.18751681X-RAY DIFFRACTION99.89
3.52-3.880.19952100.17741667X-RAY DIFFRACTION100
3.88-4.430.17381910.15671713X-RAY DIFFRACTION100
4.44-5.580.18091920.15441716X-RAY DIFFRACTION100
5.58-30.920.20142160.17281746X-RAY DIFFRACTION99.49

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