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- PDB-6btf: DNA Polymerase Beta I260Q Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 6btf
TitleDNA Polymerase Beta I260Q Ternary Complex
Components
  • DNA Downstream Strand
  • DNA Primer Strand
  • DNA Template Strand
  • DNA polymerase beta
KeywordsTRANSFERASE / LYASE/DNA / Lyase / DNA complex / LYASE-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 / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-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 / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / 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 / in utero embryonic development / neuron apoptotic process / response to ethanol / 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 / nucleus / metal ion binding / 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 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 / 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'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsEckenroth, B.E. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA080830 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.
Authors: Liptak, C. / Mahmoud, M.M. / Eckenroth, B.E. / Moreno, M.V. / East, K. / Alnajjar, K.S. / Huang, J. / Towle-Weicksel, J.B. / Doublie, S. / Loria, J.P. / Sweasy, J.B.
History
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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.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_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.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

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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)47,6899
Polymers47,1284
Non-polymers5605
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-72 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 79.879, 55.382
Angle α, β, γ (deg.)90.000, 107.400, 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: 38256.645 Da / Num. of mol.: 1 / Mutation: I260Q
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: 4274.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Primer Strand


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA Downstream Strand


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 342 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / 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-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-20% PEG 3350, 175-250 mM sodium acetate, 50 mM HEPES pH 7.5, 2 mM TCEP, 1% tert-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→38 Å / Num. obs: 82376 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.76 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 12
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 8164 / CC1/2: 0.524 / Rpim(I) all: 0.301 / Rrim(I) all: 0.539 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.59 Å31.32 Å
Translation1.59 Å31.32 Å

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Processing

Software
NameVersionClassification
PHENIXv1.9-1692refinement
SAINTv2016.9-0data reduction
SADABSv2016.9-0data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 1.75→37.551 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.94
RfactorNum. reflection% reflection
Rfree0.2138 8300 10.08 %
Rwork0.1749 --
obs0.1788 82376 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.03 Å2 / Biso mean: 31.3994 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 1.75→37.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 596 32 337 3430
Biso mean--25.11 40.11 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063216
X-RAY DIFFRACTIONf_angle_d0.9614472
X-RAY DIFFRACTIONf_chiral_restr0.039497
X-RAY DIFFRACTIONf_plane_restr0.004470
X-RAY DIFFRACTIONf_dihedral_angle_d19.4361224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.40032800.36022378265897
1.7699-1.79070.33873030.32292446274998
1.7907-1.81250.32812910.31632466275799
1.8125-1.83550.32462390.2752473271299
1.8355-1.85960.27542550.258525732828100
1.8596-1.88510.25452850.226924902775100
1.8851-1.9120.25092720.214825032775100
1.912-1.94060.23192830.208524782761100
1.9406-1.97090.27272800.20925392819100
1.9709-2.00320.23283010.20424272728100
2.0032-2.03780.24382720.193225692841100
2.0378-2.07480.23323060.193424322738100
2.0748-2.11470.25072990.187725322831100
2.1147-2.15790.21062820.184524782760100
2.1579-2.20480.23172860.176525292815100
2.2048-2.25610.22592830.178324542737100
2.2561-2.31250.20542870.171425362823100
2.3125-2.3750.22112480.177225042752100
2.375-2.44490.23252570.173125032760100
2.4449-2.52380.22862710.165125462817100
2.5238-2.6140.21972970.180524742771100
2.614-2.71860.22422790.178324812760100
2.7186-2.84230.21882910.179725072798100
2.8423-2.99210.21892600.173925262786100
2.9921-3.17940.20252720.171125292801100
3.1794-3.42480.19682620.15912465272799
3.4248-3.76910.16642870.14152474276199
3.7691-4.31380.16092670.1262410267797
4.3138-5.43240.19382360.14332377261394
5.4324-37.55960.20692690.17591977224680
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)
12.53840.87970.89454.31390.81822.76610.07890.08610.0046-0.0818-0.0157-0.23670.05240.0641-0.03370.17630.02410.00730.197-0.03370.17053.5913-3.141864.8972
21.4517-0.372-0.01422.42321.24131.80010.1021-0.0052-0.0706-0.0070.1209-0.31870.2180.2868-0.23890.18980.023-0.01970.20280.01640.19816.516-4.537570.8331
35.56982.10671.25782.4835-0.38152.02380.1218-0.64010.07940.2999-0.0518-0.3855-0.0738-0.0037-0.08910.13970.0265-0.01990.2032-0.05520.2098-6.82188.12683.5518
41.6435-0.03380.45291.84480.09362.7773-0.0267-0.07410.12390.01580.02870.1907-0.1803-0.3657-0.00860.10410.02170.01070.17870.01510.1544-23.173411.841371.1789
51.45030.0149-0.22941.85890.03322.86140.01890.08450.023-0.1801-0.0285-0.0553-0.11830.02080.01840.0938-0.0014-0.00750.12480.01010.1445-15.36278.492863.0545
62.3770.4364-0.59534.4076-1.18423.4976-0.12820.432-0.0494-0.63740.0016-0.0740.145-0.31060.09230.31480.0023-0.03340.2959-0.01940.1772-16.02285.329348.9238
70.6976-0.07250.03741.2593-0.95220.7316-0.0660.14590.412-0.211-0.046-0.6005-0.27570.2834-0.02910.2487-0.06910.04390.23610.00970.39390.925219.706264.4405
81.5403-0.29470.02818.46060.19591.96550.004-0.2320.3029-0.8789-0.1972-0.527-0.199-0.04760.17160.2668-0.02150.02390.1651-0.05370.3024-0.433223.156868.5808
91.05410.8858-0.61253.6116-2.01122.82780.12540.78890.3223-1.10290.2137-0.34070.29520.15260.09850.5642-0.07640.34210.72080.01810.31458.90620.513749.6911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 47 )A11 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 126 )A48 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 151 )A127 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 239 )A152 - 239
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 300 )A240 - 300
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 335 )A301 - 335
7X-RAY DIFFRACTION7chain 'T' and (resid 3 through 16 )T3 - 16
8X-RAY DIFFRACTION8chain 'P' and (resid 1 through 10 )P1 - 10
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 5 )D1 - 5

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