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- PDB-7k96: Human DNA polymerase beta ternary complex with templating cytosin... -

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Basic information

Entry
Database: PDB / ID: 7k96
TitleHuman DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / DNA repair / polymerase / DNA BINDING PROTEIN / 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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / 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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / 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 / 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 / microtubule / in utero embryonic development / 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, 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
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVarela, F.A. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2021
Title: Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta.
Authors: Varela, F.A. / Freudenthal, B.D.
History
DepositionSep 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
T: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
A: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,87525
Polymers47,6684
Non-polymers1,20721
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-188 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.800, 80.400, 55.500
Angle α, β, γ (deg.)90.000, 107.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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DNA chain , 3 types, 3 molecules TPD

#1: DNA chain DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 4829.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#4: Protein DNA polymerase beta


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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Non-polymers , 6 types, 183 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50 mM imidazole, 350 mM sodium chloride, 16-17% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 5, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 23635 / % possible obs: 99.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 27.86 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Χ2: 0.95 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1166 / CC1/2: 0.546 / CC star: 0.841 / Rpim(I) all: 0.525 / Rrim(I) all: 0.902 / Χ2: 0.642 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 2.1→25 Å / SU ML: 0.2934 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 3207 9.84 %
Rwork0.1831 29379 -
obs0.1892 23635 65.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 629 59 162 3457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00963438
X-RAY DIFFRACTIONf_angle_d1.11184761
X-RAY DIFFRACTIONf_chiral_restr0.0649519
X-RAY DIFFRACTIONf_plane_restr0.0067505
X-RAY DIFFRACTIONf_dihedral_angle_d23.2081351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.120.1812140.2786108X-RAY DIFFRACTION5.53
2.12-2.150.3558480.2616370X-RAY DIFFRACTION19.42
2.15-2.180.3742500.2552559X-RAY DIFFRACTION28.29
2.18-2.220.3255810.2614666X-RAY DIFFRACTION33.38
2.22-2.260.2825720.2577709X-RAY DIFFRACTION37.07
2.26-2.310.335950.2601817X-RAY DIFFRACTION41.19
2.31-2.350.27991020.2424835X-RAY DIFFRACTION44.79
2.35-2.40.29281110.2467952X-RAY DIFFRACTION47.41
2.4-2.460.30711140.2405974X-RAY DIFFRACTION51.59
2.46-2.520.32581170.22791132X-RAY DIFFRACTION57.14
2.52-2.590.28261210.24151181X-RAY DIFFRACTION60.47
2.59-2.660.30181360.24151290X-RAY DIFFRACTION65.93
2.66-2.750.30291560.24081401X-RAY DIFFRACTION71.36
2.75-2.850.30141670.24171566X-RAY DIFFRACTION79.68
2.85-2.960.31452200.24351658X-RAY DIFFRACTION85.52
2.96-3.10.40671930.22871771X-RAY DIFFRACTION91.35
3.1-3.260.28622170.20721877X-RAY DIFFRACTION96.36
3.26-3.460.21011870.17291920X-RAY DIFFRACTION97.37
3.46-3.730.21421740.16091919X-RAY DIFFRACTION97.9
3.73-4.10.19932100.14161926X-RAY DIFFRACTION98.16
4.11-4.70.21312070.13641919X-RAY DIFFRACTION97.93
4.7-5.90.18282150.14671905X-RAY DIFFRACTION97.74
5.9-25.090.20772000.15641924X-RAY DIFFRACTION97.52
Refinement TLS params.Method: refined / Origin x: 9.01243311652 Å / Origin y: 7.80171088861 Å / Origin z: 14.8747910388 Å
111213212223313233
T0.189452108528 Å2-0.034676986171 Å2-0.00242332087521 Å2-0.148948274567 Å20.000902430094863 Å2--0.142845225724 Å2
L1.69959297617 °2-0.806610027031 °20.0213150659358 °2-0.966657131617 °20.20464427469 °2--0.750575329141 °2
S0.0262014733457 Å °0.110655024387 Å °0.116455997353 Å °-0.0960226128994 Å °-0.0383403337514 Å °-0.0758575324139 Å °-0.0298819158483 Å °0.0114683488311 Å °0.0112101444884 Å °
Refinement TLS groupSelection details: all

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