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- PDB-4klu: DNA polymerase beta mismatched product complex with Mn2+, 15 h -

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Basic information

Entry
Database: PDB / ID: 4klu
TitleDNA polymerase beta mismatched product complex with Mn2+, 15 h
Components
  • 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3'
  • 5'-D(P*GP*TP*CP*GP*G)-3'
  • DNA polymerase beta
KeywordsTRANSFERASE / LYASE/DNA / DNA polymerase / 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 / 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
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 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 / Beta Polymerase, domain 2 / 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 (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsFreudenthal, B.D. / Beard, W.A. / Shock, D.D. / Wilson, S.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Observing a DNA polymerase choose right from wrong.
Authors: Freudenthal, B.D. / Beard, W.A. / Shock, D.D. / Wilson, S.H.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 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_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.ptnr2_auth_asym_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_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_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*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
P: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3'
D: 5'-D(P*GP*TP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1778
Polymers48,0214
Non-polymers1564
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-54 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.222, 80.105, 55.812
Angle α, β, γ (deg.)90.000, 109.640, 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: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Polb / Plasmid: pWL11 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap56
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 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'


Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3'


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(P*GP*TP*CP*GP*G)-3'


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 302 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2012 / Details: vertical focusing mirrors
Diffraction measurementDetails: 0.50 degrees, 1.6 sec, detector distance 200.00 mm
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.052 / Number: 112092
ReflectionResolution: 1.97→50 Å / Num. all: 32458 / Num. obs: 31557 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Χ2: 1.072 / Net I/σ(I): 16
Reflection shellResolution: 1.97→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.429 / Rsym value: 0.227 / % possible all: 75.3
Cell measurementReflection used: 112092

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ISB

3isb


Resolution: 1.97→31.985 Å / Occupancy max: 1 / Occupancy min: 0.62 / FOM work R set: 0.8059 / SU ML: 0.31 / σ(F): 0 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1509 4.95 %
Rwork0.2115 --
obs0.2135 30436 91.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.878 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 82.39 Å2 / Biso mean: 35.0063 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--7.3675 Å20 Å2-2.7973 Å2
2--1.9221 Å2-0 Å2
3---5.4455 Å2
Refinement stepCycle: LAST / Resolution: 1.97→31.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 653 4 298 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073373
X-RAY DIFFRACTIONf_angle_d1.1114678
X-RAY DIFFRACTIONf_chiral_restr0.069516
X-RAY DIFFRACTIONf_plane_restr0.004491
X-RAY DIFFRACTIONf_dihedral_angle_d20.5961321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.00220.2808790.24671535161453
2.0022-2.03670.2857890.24691825191464
2.0367-2.07370.35411100.26142103221372
2.0737-2.11360.28631280.24872326245481
2.1136-2.15670.2521290.24232505263487
2.1567-2.20360.25781430.23492593273691
2.2036-2.25480.29671430.23392657280093
2.2548-2.31120.30581450.23712732287794
2.3112-2.37370.31941270.22752776290395
2.3737-2.44350.28761560.23342751290797
2.4435-2.52240.27691490.22782832298197
2.5224-2.61250.28731360.24222775291198
2.6125-2.7170.31111500.242822297298
2.717-2.84060.29291480.24122880302899
2.8406-2.99030.28661460.23732822296899
2.9903-3.17740.24011550.213428913046100
3.1774-3.42250.26331480.20629093057100
3.4225-3.76650.22331570.188828693026100
3.7665-4.31040.20561500.173928763026100
4.3104-5.42630.20961540.183128613015100
5.4263-31.9890.20821350.20012869300499

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