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- PDB-3uxn: Crystal Structure of Rat DNA Polymerase Beta, Wild Type Apoenzyme -

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Basic information

Entry
Database: PDB / ID: 3uxn
TitleCrystal Structure of Rat DNA Polymerase Beta, Wild Type Apoenzyme
ComponentsDNA polymerase beta
KeywordsTRANSFERASE / DNA Polymerase / Base Excision Repair
Function / homology
Function and homology information


Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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 / DNA replication / in utero embryonic development / 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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGridley, C.L. / Firbank, S. / Jaeger, J.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta.
Authors: Gridley, C.L. / Rangarajan, S. / Firbank, S. / Dalal, S. / Sweasy, J.B. / Jaeger, J.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)76,7782
Polymers76,7782
Non-polymers00
Water2,864159
1
A: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)38,3891
Polymers38,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)38,3891
Polymers38,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.946, 67.447, 83.357
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase beta


Mass: 38388.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Polb / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 8, 2008
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15.002 Å / Num. obs: 22615 / % possible obs: 83.93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.5674177
2.5674-2.6425181
2.6425-2.7273183
2.7273-2.8242187
2.8242-2.9365188
2.9365-3.069189

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15.002 Å / SU ML: 0.52 / σ(F): 0.07 / Phase error: 31.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3166 1815 8.03 %random
Rwork0.25 ---
all0.2521 ---
obs0.2554 22615 83.93 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.972 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1587 Å2-0 Å20.3356 Å2
2---3.5404 Å2-0 Å2
3---6.6991 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 0 159 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095318
X-RAY DIFFRACTIONf_angle_d1.2717158
X-RAY DIFFRACTIONf_dihedral_angle_d18.32066
X-RAY DIFFRACTIONf_chiral_restr0.08782
X-RAY DIFFRACTIONf_plane_restr0.004934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56740.42011410.34051437X-RAY DIFFRACTION77
2.5674-2.64250.38511200.30191545X-RAY DIFFRACTION81
2.6425-2.72730.33571410.29111567X-RAY DIFFRACTION83
2.7273-2.82420.33971400.25321658X-RAY DIFFRACTION87
2.8242-2.93650.3771420.26261686X-RAY DIFFRACTION88
2.9365-3.0690.32681560.25931674X-RAY DIFFRACTION89
3.069-3.22930.36691440.24961688X-RAY DIFFRACTION89
3.2293-3.42940.35581510.26591660X-RAY DIFFRACTION88
3.4294-3.69050.4389980.37151132X-RAY DIFFRACTION59
3.6905-4.05520.31661130.27951399X-RAY DIFFRACTION73
4.0552-4.62690.25621580.19041780X-RAY DIFFRACTION93
4.6269-5.77360.25481550.2051793X-RAY DIFFRACTION93
5.7736-15.00230.2281560.17931781X-RAY DIFFRACTION91

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