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- PDB-3ogu: DNA Polymerase beta mutant 5P20 complexed with 6bp of DNA -

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Basic information

Entry
Database: PDB / ID: 3ogu
TitleDNA Polymerase beta mutant 5P20 complexed with 6bp of DNA
Components
  • 5'-D(*CP*AP*TP*CP*TP*G)-3'
  • 5'-D(P*CP*AP*GP*AP*TP*G)-3'
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / DNA Polymerase / DNA repair / 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 / PCNA-Dependent Long Patch Base Excision Repair / 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 / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / 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
DNA / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 Å
AuthorsMarx, A. / Diederichs, K. / Bergen, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Human DNA polymerase beta mutations allowing efficient abasic site bypass.
Authors: Gieseking, S. / Bergen, K. / Di Pasquale, F. / Diederichs, K. / Welte, W. / Marx, A.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / 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_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 / _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: 5'-D(*CP*AP*TP*CP*TP*G)-3'
P: 5'-D(P*CP*AP*GP*AP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1848
Polymers41,8273
Non-polymers3565
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-9 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.474, 56.782, 47.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21A-595-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta /


Mass: 38209.762 Da / Num. of mol.: 1 / Mutation: S2G,F99L,E232K,V269M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 AI
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 2 types, 2 molecules TP

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


Mass: 1784.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide
#3: DNA chain 5'-D(P*CP*AP*GP*AP*TP*G)-3'


Mass: 1833.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide

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Non-polymers , 4 types, 340 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 10% PEG 3350, 0.1 M sodium chloride, 0.1 M MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2008
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.845→47.677 Å / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.1
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.43 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)model building
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.6.1_357phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9ICW

9icw


Resolution: 1.845→47.67 Å / SU ML: 0.28 / Isotropic thermal model: isotropic and tls / σ(F): 2 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2100 5.07 %
Rwork0.197 --
obs0.1988 41382 98.74 %
all-41386 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.742 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2459 Å
Refinement stepCycle: LAST / Resolution: 1.845→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 244 21 335 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022949
X-RAY DIFFRACTIONf_angle_d0.6364012
X-RAY DIFFRACTIONf_dihedral_angle_d14.631158
X-RAY DIFFRACTIONf_chiral_restr0.043437
X-RAY DIFFRACTIONf_plane_restr0.002474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8454-1.88840.34831290.31742171X-RAY DIFFRACTION84
1.8884-1.93560.31971490.28452511X-RAY DIFFRACTION98
1.9356-1.98790.30931340.26832642X-RAY DIFFRACTION100
1.9879-2.04640.32171400.24742605X-RAY DIFFRACTION100
2.0464-2.11250.24491450.22442609X-RAY DIFFRACTION100
2.1125-2.1880.23451460.20472624X-RAY DIFFRACTION100
2.188-2.27560.24881470.2112614X-RAY DIFFRACTION100
2.2756-2.37910.24841240.21652642X-RAY DIFFRACTION100
2.3791-2.50460.28931110.21672663X-RAY DIFFRACTION100
2.5046-2.66150.27461370.21922635X-RAY DIFFRACTION100
2.6615-2.86690.25461490.20612637X-RAY DIFFRACTION100
2.8669-3.15540.25931430.19982688X-RAY DIFFRACTION100
3.1554-3.61180.20481540.17362649X-RAY DIFFRACTION100
3.6118-4.550.17191240.15862741X-RAY DIFFRACTION100
4.55-47.68560.22291680.1952851X-RAY DIFFRACTION100
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)
10.91870.00780.67761.61660.2250.61980.0333-0.02620.13390.0017-0.07010.17110.16840.129-00.2145-0.03380.00920.226-0.00820.216652.198152.349960.3269
21.5286-0.1484-0.78450.5278-0.13720.72110.0196-0.064-0.1703-0.0223-0.04670.0515-0.05080.102600.1367-0.0464-0.01910.230100.049569.38823.323852.9345
30.9778-0.2942-0.16020.6932-0.54021.1969-0.01860.37090.20980.122-0.10840.0088-0.1168-0.138500.2268-0.0265-0.06760.26620.12980.126472.890941.933434.0942
40.09510.0153-0.12030.0290.04480.2415-0.4284-0.3274-0.1553-0.32420.01350.0608-0.8741-0.1043-00.2383-0.0322-0.05130.2732-0.01910.279750.009826.414946.9374
50.2846-0.16580.26140.0560.08360.07380.18110.1730.0524-0.3694-0.07880.29970.18940.157700.1628-0.0704-0.0510.2770.00250.227354.487820.916845.6279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:92)
2X-RAY DIFFRACTION2(chain A and resid 93:255)
3X-RAY DIFFRACTION3(chain A and resid 256:335)
4X-RAY DIFFRACTION4(chain P and resid 1:6)
5X-RAY DIFFRACTION5(chain T and resid 2:7)

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