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- PDB-7k97: Human DNA polymerase beta dGDP product complex with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 7k97
TitleHuman DNA polymerase beta dGDP product complex with Mn2+
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*CP*G)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / Polymerase / nucleotide analog / 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 / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity ...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 / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision 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 / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / 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 / Ub-specific processing proteases / lyase activity / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / 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 family X, binding site ...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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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)R35-GM128562 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
A: DNA polymerase beta
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*G)-3')
T: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,51815
Polymers46,9384
Non-polymers58011
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-100 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.102, 77.309, 55.111
Angle α, β, γ (deg.)90.000, 114.847, 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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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 37182.410 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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DNA chain , 3 types, 3 molecules DPT

#2: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*G)-3')


Mass: 3390.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: 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: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 4 types, 67 molecules

#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 45.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 50 mM imidazole, 350 mM sodium acetate, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16511 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 36.2 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.093 / Χ2: 0.933 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 804 / CC1/2: 0.54 / CC star: 0.837 / Rpim(I) all: 0.517 / Rrim(I) all: 0.961 / Χ2: 0.99 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
HKL-3000data scaling
PHENIX1.19rc5_4047phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 2.4→30.58 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4916
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 2493 10.04 %
Rwork0.1852 22347 -
obs0.1907 16511 76.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.41 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 651 15 56 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933424
X-RAY DIFFRACTIONf_angle_d1.08874749
X-RAY DIFFRACTIONf_chiral_restr0.0682519
X-RAY DIFFRACTIONf_plane_restr0.0088505
X-RAY DIFFRACTIONf_dihedral_angle_d22.7351355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.368500.3762464X-RAY DIFFRACTION28.65
2.45-2.50.4451740.3366619X-RAY DIFFRACTION37.56
2.5-2.550.3647760.288701X-RAY DIFFRACTION45.73
2.55-2.610.3065920.2666833X-RAY DIFFRACTION51.36
2.61-2.670.28871050.2559904X-RAY DIFFRACTION56.69
2.68-2.750.27111190.25591031X-RAY DIFFRACTION61.99
2.75-2.830.34571170.23751089X-RAY DIFFRACTION68.37
2.83-2.920.33981250.231199X-RAY DIFFRACTION74.09
2.92-3.020.2991420.22691338X-RAY DIFFRACTION81.9
3.02-3.140.31561720.21451464X-RAY DIFFRACTION91.5
3.14-3.290.28421780.19641569X-RAY DIFFRACTION96.25
3.29-3.460.24111780.18671609X-RAY DIFFRACTION98.89
3.46-3.680.2321660.16941602X-RAY DIFFRACTION99.21
3.68-3.960.20081830.15691610X-RAY DIFFRACTION99.17
3.96-4.360.1991770.1451551X-RAY DIFFRACTION99.2
4.36-4.990.2231760.15561638X-RAY DIFFRACTION99.34
4.99-6.270.21631790.17861575X-RAY DIFFRACTION98.93
6.27-30.580.18171840.16161551X-RAY DIFFRACTION97.04
Refinement TLS params.Method: refined / Origin x: 3.40193329624 Å / Origin y: -9.45776770914 Å / Origin z: 13.1964007502 Å
111213212223313233
T0.242937085904 Å2-0.029787479149 Å2-0.0144622556764 Å2-0.25614128498 Å20.0569237141326 Å2--0.208927061532 Å2
L1.66532888013 °2-0.157097288953 °2-0.252192404846 °2-1.51613072727 °20.221656589428 °2--2.37862885592 °2
S0.0662617601558 Å °0.0916437396185 Å °-0.0184375841421 Å °-0.0689126092042 Å °0.0200043167685 Å °0.0502362361422 Å °-0.0130195914132 Å °-0.227490691243 Å °-0.0773150853632 Å °
Refinement TLS groupSelection details: all

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