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- PDB-4m9n: DNA Polymerase Beta E295K Soaked with dATP -

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Basic information

Entry
Database: PDB / ID: 4m9n
TitleDNA Polymerase Beta E295K Soaked with dATP
Components
  • DNA Downstream Strand
  • DNA Primer Strand
  • DNA Template Strand
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / DNA Polymerase / Lyase / DNA complex / TRANSFERASE-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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / 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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / 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
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 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Isomorphous replacement / Resolution: 2.275 Å
AuthorsEckenroth, B.E. / Doublie, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection.
Authors: Eckenroth, B.E. / Towle-Weicksel, J.B. / Sweasy, J.B. / Doublie, S.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 Template Strand
P: DNA Primer Strand
D: DNA Downstream Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2538
Polymers47,6924
Non-polymers5614
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-50 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.523, 79.215, 54.685
Angle α, β, γ (deg.)90.000, 106.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta /


Mass: 38241.738 Da / Num. of mol.: 1 / Mutation: E295K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 DE3
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA Template Strand


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Template Strand, 16mer
#3: DNA chain DNA Primer Strand


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Primer Strand, 10mer
#4: DNA chain DNA Downstream Strand


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Downstream Strand, 5mer

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Non-polymers , 4 types, 238 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 16, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.275→14 Å / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.48 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.073 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.275-2.362.30.24516571.143181.9
2.36-2.462.80.21719051.123193.7
2.46-2.573.20.19420301.129199.3
2.57-2.73.40.15520231.133199.9
2.7-2.873.50.11420461.07199.9
2.87-3.093.50.08820291.051100
3.09-3.393.60.06120531.0571100
3.39-3.883.60.04520651.0441100
3.88-4.853.60.03520371.036199.9
4.85-143.50.02621061.015199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: Isomorphous replacement / Resolution: 2.275→13.923 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8112 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 3646 9.94 %
Rwork0.1915 --
obs0.1951 36691 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.19 Å2 / Biso mean: 34.6408 Å2 / Biso min: 11.72 Å2
Refinement stepCycle: LAST / Resolution: 2.275→13.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 627 33 234 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023101
X-RAY DIFFRACTIONf_angle_d0.5984320
X-RAY DIFFRACTIONf_chiral_restr0.036483
X-RAY DIFFRACTIONf_plane_restr0.002444
X-RAY DIFFRACTIONf_dihedral_angle_d17.4681213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2751-2.30490.3147920.2574083254
2.3049-2.33630.29561090.2485939104867
2.3363-2.36950.33291260.24421017114374
2.3695-2.40470.2921820.24361122120479
2.4047-2.44210.29041300.22871166129685
2.4421-2.48190.28571310.23481283141490
2.4819-2.52450.33131400.2341291143192
2.5245-2.57010.29591430.24081310145394
2.5701-2.61920.30381500.22181307145794
2.6192-2.67230.29221490.22351296144595
2.6723-2.730.26961600.23131346150695
2.73-2.7930.30461750.21451264143996
2.793-2.86230.22661300.21971381151196
2.8623-2.93890.26091210.21381369149095
2.9389-3.02460.2631460.22091358150497
3.0246-3.12110.26391370.21161319145696
3.1211-3.23130.26141670.19861320148796
3.2313-3.3590.26261650.19371339150497
3.359-3.50950.20071090.18871369147897
3.5095-3.69130.22781570.17011366152397
3.6913-3.91770.21281670.17261345151297
3.9177-4.21240.15761510.1591370152198
4.2124-4.62220.17571320.14861348148098
4.6222-5.25920.17111450.15411341148698
5.2592-6.51130.1851480.18491396154498
6.5113-13.9230.18171840.17921343152798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.25750.04170.26723.9671.79483.41650.02010.0093-0.4021-0.3723-0.0072-0.16260.2836-0.19380.00170.2445-0.03170.02740.14780.02210.214530.5791-4.34647.8729
24.0193-2.3676-1.67992.42831.02671.7374-0.0465-0.5955-0.0675-0.06540.0785-0.34210.02690.4076-0.04760.1814-0.0352-0.01050.29620.04820.25633.62451.397223.2442
35.27010.22580.92221.6582-0.2461.63640.0881-0.0993-0.1118-0.048-0.01890.12420.0457-0.1578-0.05890.12830.01690.03020.1438-0.01540.13644.70859.228521.8968
43.9013-0.7245-1.24024.0724-0.04723.45230.00950.04890.2882-0.23590.063-0.29110.02240.345-0.04830.5340.14040.07160.340.04060.208732.052813.9581-2.9452
52.14950.69720.38295.93390.02971.40450.03330.24660.2159-0.2270.0769-0.5095-0.10820.142-0.0810.26210.01550.030.16970.02710.323716.417724.328514.9497
62.3868-1.1577-0.88147.32040.55913.71490.1027-0.11070.4033-0.7948-0.35110.0165-0.2272-0.16310.27050.2107-0.0431-0.05840.1853-0.03680.289416.913225.567115.8491
73.9595-0.8477-1.08446.5321-2.8234.77020.15370.54630.2025-0.60240.020.54010.4647-0.2898-0.19510.3967-0.0753-0.0340.23940.09140.219231.58656.2669-4.1075
81.14561.2985-1.17584.8399-2.06243.7942-0.47490.7971-0.3609-1.20330.589-0.35590.4763-0.1231-0.13310.5074-0.17650.06660.7217-0.16990.40323.30247.1827-2.1997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10:79)A10 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80:102)A80 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103:261)A103 - 261
4X-RAY DIFFRACTION4chain 'T' and (resid 1:5)T1 - 5
5X-RAY DIFFRACTION5chain 'T' and (resid 6:16)T6 - 16
6X-RAY DIFFRACTION6chain 'P' and (resid 1:10)P1 - 10
7X-RAY DIFFRACTION7chain 'D' and (resid 1:5)D1 - 5
8X-RAY DIFFRACTION8chain 'A' and (resid 262:333)A262 - 333

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