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- PDB-7m08: Post-catalytic nicked complex of DNA Polymerase Lambda with bound... -

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Basic information

Entry
Database: PDB / ID: 7m08
TitlePost-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE / Nonhomologous end-joining / Base Excision Repair
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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
ACETATE ION / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKaminski, A.M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
CitationJournal: Not Published
Title: Comprehensive structural survey of DNA double-strand break synapsis by DNA Polymerase Lambda
Authors: Kaminski, A.M. / Bebenek, K. / Kunkel, T.A. / Pedersen, L.C.
History
DepositionMar 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_abbrev

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
T: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,50012
Polymers45,2144
Non-polymers2858
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-95 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.136, 59.862, 140.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 38550.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: Q9UGP5, 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 (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')


Mass: 2097.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 344 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2020
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 52904 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.57 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rsym value: 0.078 / Χ2: 1.008 / Net I/σ(I): 26.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 2579 / CC1/2: 0.829 / CC star: 0.952 / Rsym value: 0.677 / Χ2: 0.38 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFO

2pfo


Resolution: 1.7→43.82 Å / SU ML: 0.2128 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2642 5 %random
Rwork0.1855 50193 --
obs0.1867 52835 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.17 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 446 14 336 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663130
X-RAY DIFFRACTIONf_angle_d0.82384349
X-RAY DIFFRACTIONf_chiral_restr0.0509481
X-RAY DIFFRACTIONf_plane_restr0.0055488
X-RAY DIFFRACTIONf_dihedral_angle_d12.4859935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.34931260.3342548X-RAY DIFFRACTION98.74
1.73-1.760.31011560.28542619X-RAY DIFFRACTION99.89
1.76-1.80.2621290.25372595X-RAY DIFFRACTION99.89
1.8-1.840.261360.22582616X-RAY DIFFRACTION99.82
1.84-1.880.2171450.20182603X-RAY DIFFRACTION99.93
1.88-1.930.21321360.18372628X-RAY DIFFRACTION99.86
1.93-1.980.21471150.18712623X-RAY DIFFRACTION99.82
1.98-2.040.20631490.19212597X-RAY DIFFRACTION99.75
2.04-2.10.22361500.20132620X-RAY DIFFRACTION99.86
2.1-2.180.22521220.21222637X-RAY DIFFRACTION99.86
2.18-2.270.2321470.19922620X-RAY DIFFRACTION99.93
2.27-2.370.20471380.18342639X-RAY DIFFRACTION100
2.37-2.490.19941420.17772668X-RAY DIFFRACTION100
2.49-2.650.2111380.18522636X-RAY DIFFRACTION99.78
2.65-2.850.21941380.19312645X-RAY DIFFRACTION99.5
2.85-3.140.19721380.18812673X-RAY DIFFRACTION99.96
3.14-3.60.19411460.17242674X-RAY DIFFRACTION100
3.6-4.530.17661390.14742709X-RAY DIFFRACTION99.44
4.53-43.820.21121520.18212843X-RAY DIFFRACTION99.27
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)
10.4035532521870.20699358153-0.07029412304830.666999924763-0.1608731041870.770425047615-0.1014572406330.306171934050.00319626199538-0.2942104047260.308057476208-0.274287579474-0.108908616630.25870902030.002056900004380.375791249659-0.09055599126970.1028571287480.393643344884-0.03229406525630.287637117681-7.5116313198726.3965292426-25.7281287456
20.5315560884190.2848999219550.01553166497830.723746625683-0.06077208498120.45633813123-0.0221422503621-0.1099619567460.1356785689990.009964969700840.0736324483088-0.04252301461860.043681353052-0.1258706966270.002917566928080.1356235144920.00377344350226-0.00773413198840.141738942704-0.02902274976730.154253599047-13.461322450320.09981155370.671731758455
30.791687945469-0.6001877369610.3288583917891.02183601236-0.2026938133851.721259553910.0491021130283-0.0201131380734-0.302649220689-0.01775167994870.02583057317360.05878449533880.1513729132880.0268639493028-0.0009531249287820.162327839895-0.0179083714817-0.01478643679040.125569620741-0.01910998688990.240939307606-12.2044205794-5.13714810062-7.469537146
40.736150240573-0.2570660409070.0370466423640.404720905899-0.01891482697010.5353653881690.08120225091820.319562970637-0.108316398787-0.300596234149-0.0310139918793-0.01651885254690.01795263425930.1126554412230.0340253865360.2491087364310.0290073995665-0.02530416657950.243573941706-0.05647172349130.161047674884-18.99265969451.80973233541-27.8341262009
50.5812507461230.244956837821-0.414275208820.2132618173940.5479605252270.560615130034-0.004211117677660.167266754493-0.0173046407749-0.095639143910.008262895844750.2060850634-0.101407289764-0.15237985373-0.03895930779770.1647969240740.0265423970592-0.02371830259420.199421288403-0.0006427535308490.143280885628-25.019295576616.384253741-18.0297261724
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 239:329AA239 - 3291 - 91
22chain A and resid 330:386AA330 - 38692 - 148
33chain A and resid 387:495AA387 - 495149 - 257
44chain A and resid 496:575AA496 - 575258 - 325
55chain T or chain P or chain DT - DB - D1 - 4

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