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- PDB-9ewg: DNA Polymerase Lambda I493K, TTP:At Ca2+ Ground State Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 9ewg
TitleDNA Polymerase Lambda I493K, TTP:At Ca2+ Ground State Ternary Complex
Components
  • (DNA primer strand ...) x 2
  • DNA polymerase lambda
  • DNA template strand
KeywordsNUCLEAR PROTEIN / DNA polymerase Gap filling
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
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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNourisson, A. / Haouz, A. / Missoury, S. / Delarue, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair.
Authors: Nourisson, A. / Missoury, S. / Lucas-Staat, S. / Haouz, A. / Delarue, M.
History
DepositionApr 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
D: DNA primer strand downstream
P: DNA primer strand upstream
T: DNA template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,98015
Polymers43,1684
Non-polymers81211
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, DNA polymerase assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-75 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.042, 62.504, 141.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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DNA primer strand ... , 2 types, 2 molecules DP

#2: DNA chain DNA primer strand downstream


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA primer strand upstream


Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / DNA chain , 2 types, 2 molecules AT

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


Mass: 36809.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#4: DNA chain DNA template strand


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 259 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM bicine pH7.5 300 mM Na-K tartrate 17.5% PEG 20K 10 mM praseodyme acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.916→70.7 Å / Num. obs: 25444 / % possible obs: 93.3 % / Redundancy: 11.9 % / CC1/2: 0.996 / Rpim(I) all: 0.052 / Net I/σ(I): 11
Reflection shellResolution: 1.916→2.118 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1272 / CC1/2: 0.504 / Rpim(I) all: 0.807

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.7 Å / SU ML: 0.2427 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 1978 7.86 %RANDOM
Rwork0.2046 23188 --
obs0.2083 25166 73.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.31 Å2
Refinement stepCycle: LAST / Resolution: 2→70.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 426 48 248 3131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523001
X-RAY DIFFRACTIONf_angle_d0.73344141
X-RAY DIFFRACTIONf_chiral_restr0.0485458
X-RAY DIFFRACTIONf_plane_restr0.0062457
X-RAY DIFFRACTIONf_dihedral_angle_d21.0861154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.3782280.2815320X-RAY DIFFRACTION14.49
2.05-2.110.3229410.2458476X-RAY DIFFRACTION21.51
2.11-2.170.2931630.2552747X-RAY DIFFRACTION33.58
2.17-2.240.3239950.25271101X-RAY DIFFRACTION49.12
2.24-2.320.29761120.25721319X-RAY DIFFRACTION59.21
2.32-2.410.25971290.2681522X-RAY DIFFRACTION68.11
2.41-2.520.31871540.25221796X-RAY DIFFRACTION80.61
2.52-2.650.28091790.2492094X-RAY DIFFRACTION93.08
2.65-2.820.30451920.24462257X-RAY DIFFRACTION100
2.82-3.040.25441910.22482240X-RAY DIFFRACTION100
3.04-3.340.25681930.19732277X-RAY DIFFRACTION99.96
3.34-3.830.24231960.17192292X-RAY DIFFRACTION100
3.83-4.820.17941970.15952313X-RAY DIFFRACTION100
4.82-70.70.2692080.21122434X-RAY DIFFRACTION99.92
Refinement TLS params.Method: refined / Origin x: -15.2609153908 Å / Origin y: -12.0400984095 Å / Origin z: 15.2886038817 Å
111213212223313233
T0.111877432137 Å20.0425503039336 Å2-0.0292911045061 Å2-0.207977570811 Å2-0.0394974151833 Å2--0.133469953165 Å2
L3.02803598871 °2-0.000803924478759 °2-1.33556684604 °2-1.97156244965 °20.367707592879 °2--1.97677560838 °2
S0.0642073502911 Å °-0.442086354869 Å °0.20819810542 Å °0.31258762145 Å °0.155654578738 Å °-0.0326573180825 Å °0.0315362484735 Å °0.217289346511 Å °-0.092741519157 Å °
Refinement TLS groupSelection details: all

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