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- PDB-9ewb: DNA Polymerase Lambda I493R, TTP:At Ca2+ Ground State Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 9ewb
TitleDNA Polymerase Lambda I493R, TTP:At Ca2+ Ground State Ternary Complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*C)-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
KeywordsNUCLEAR PROTEIN / DNA repair / Gap-filling / NHEJ / DNA polymerase
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'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
F: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
G: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
H: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,16715
Polymers43,1644
Non-polymers1,00311
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, DNA polymerase activity assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-45 kcal/mol
Surface area17480 Å2
Unit cell
Length a, b, c (Å)56.280, 62.510, 140.220
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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Protein , 1 types, 1 molecules A

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


Mass: 36805.062 Da / Num. of mol.: 1 / Mutation: I493R
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

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DNA chain , 3 types, 3 molecules FGH

#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.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')


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

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Non-polymers , 5 types, 311 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM bicine pH 7,5, 300 mM Na-K tartrate, 22,5% PEG Smear high

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.32→46.74 Å / Num. obs: 22111 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.85
Reflection shellResolution: 2.32→2.38 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 3488 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
ADDREFdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→41.83 Å / SU ML: 0.301 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1999 9.05 %RANDOM
Rwork0.2037 20098 --
obs0.2056 22097 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.97 Å2
Refinement stepCycle: LAST / Resolution: 2.32→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 426 60 300 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983094
X-RAY DIFFRACTIONf_angle_d1.40214263
X-RAY DIFFRACTIONf_chiral_restr0.0822468
X-RAY DIFFRACTIONf_plane_restr0.0131474
X-RAY DIFFRACTIONf_dihedral_angle_d21.34461198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.31781370.30681373X-RAY DIFFRACTION98.63
2.38-2.440.36461420.27351424X-RAY DIFFRACTION99.94
2.44-2.510.27361390.24561402X-RAY DIFFRACTION99.81
2.51-2.60.29141410.22791424X-RAY DIFFRACTION99.94
2.6-2.690.26431420.23141427X-RAY DIFFRACTION99.94
2.69-2.80.3151400.26081407X-RAY DIFFRACTION99.94
2.8-2.920.31861410.23811417X-RAY DIFFRACTION99.94
2.92-3.080.23081400.2121418X-RAY DIFFRACTION100
3.08-3.270.22941440.20151440X-RAY DIFFRACTION99.94
3.27-3.520.22561430.20481440X-RAY DIFFRACTION99.94
3.52-3.880.21271430.17241426X-RAY DIFFRACTION100
3.88-4.440.19041450.16091468X-RAY DIFFRACTION100
4.44-5.590.17651460.17631472X-RAY DIFFRACTION100
5.59-41.830.21591560.22921560X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.2409025871 Å / Origin y: -11.7442432541 Å / Origin z: 15.5042838366 Å
111213212223313233
T0.382851390985 Å20.00671701913833 Å2-0.0176059930206 Å2-0.391984636948 Å2-0.0367026246566 Å2--0.346168898452 Å2
L1.47845841722 °20.178051939637 °2-0.561932236568 °2-0.949267972799 °2-0.0840151640376 °2--0.305108857844 °2
S0.0629239272238 Å °-0.241778851934 Å °0.0770436796601 Å °0.12516732707 Å °0.0209968438772 Å °-0.00943494798629 Å °0.0173439369069 Å °0.117295796303 Å °6.21936919621E-5 Å °
Refinement TLS groupSelection details: all

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