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- PDB-9ewc: DNA Polymerase Lambda I493R 528-530 NEY, TTP:At Ca2+ Ground State... -

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Basic information

Entry
Database: PDB / ID: 9ewc
TitleDNA Polymerase Lambda I493R 528-530 NEY, 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
DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.67 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
C: DNA polymerase lambda
E: DNA template strand
F: DNA template strand
G: DNA primer strand upstream
H: DNA primer strand downstream (5'P)
I: DNA primer strand upstream
J: DNA primer strand downstream (5'P)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,60413
Polymers86,4338
Non-polymers1715
Water905
1
A: DNA polymerase lambda
F: DNA template strand
G: DNA primer strand upstream
H: DNA primer strand downstream (5'P)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3027
Polymers43,2164
Non-polymers863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA polymerase lambda
E: DNA template strand
I: DNA primer strand upstream
J: DNA primer strand downstream (5'P)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3016
Polymers43,2164
Non-polymers852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.904, 149.904, 272.154
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 250 through 253 or (resid 254...
d_2ens_1(chain "C" and (resid 250 through 252 or (resid 253...
d_1ens_2chain "E"
d_2ens_2chain "F"
d_1ens_3chain "G"
d_2ens_3chain "I"
d_1ens_4chain "H"
d_2ens_4chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1THRTHRARGARGAA250 - 32310 - 83
d_12ens_1ASPASPASNASNAA326 - 40786 - 167
d_13ens_1GLYGLYVALVALAA409 - 537169 - 292
d_14ens_1ALAALATRPTRPAA543 - 575298 - 330
d_21ens_1THRTHRPROPROCB250 - 30310 - 63
d_22ens_1ILEILEASNASNCB305 - 40765 - 167
d_23ens_1GLYGLYVALVALCB409 - 537169 - 292
d_24ens_1ALAALATRPTRPCB543 - 575298 - 330
d_11ens_2DCDCDGDGEC1 - 21 - 2
d_21ens_2DCDCDGDGFD1 - 21 - 2
d_11ens_3DCDCDCDCGE11
d_21ens_3DCDCDCDCIG11
d_11ens_4DGDGDGDGHF11
d_21ens_4DGDGDGDGJH11

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(0.472898289694, 0.876722016583, -0.0878960365654), (0.877727916152, -0.477470551906, -0.0401942442297), (-0.0772069479453, -0.0581410156608, -0.995318396036)-51.2544759567, 90.2853888221, 2.51760235187
2given(0.472826554398, 0.878992622879, -0.0617010403548), (0.878099824147, -0.475856779131, -0.050010244835), (-0.0733194946106, -0.0305335009353, -0.99684098884)-55.2751631656, 87.8305233296, 1.16194716264
3given(0.508067503058, 0.858092469863, -0.0744629135951), (0.858095606849, -0.511742426314, -0.042327516081), (-0.0744267548906, -0.0423910636232, -0.996325075405)-49.5952291753, 91.7788694858, 1.64227704385
4given(0.450713477194, 0.890010271107, -0.0688409674491), (0.892047727635, -0.451934576902, -0.00244741136449), (-0.0332898347497, -0.060306347295, -0.997624644532)-52.0201164545, 90.2767154732, 3.48427282162

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Components

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DNA primer strand ... , 2 types, 4 molecules GIHJ

#3: DNA chain DNA primer strand upstream


Mass: 1793.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA primer strand downstream (5'P)


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / DNA chain , 2 types, 4 molecules ACEF

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


Mass: 36857.113 Da / Num. of mol.: 2 / Mutation: I493R,[528-530] NEY
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
#2: DNA chain DNA template strand


Mass: 3374.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 10 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.47 Å3/Da / Density % sol: 64.58 %
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 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.543→117.173 Å / Num. obs: 106687 / % possible obs: 91.7 % / Redundancy: 17.7 % / CC1/2: 0.85 / Rpim(I) all: 0.658 / Net I/σ(I): 7.8
Reflection shellResolution: 3.543→4.018 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4580 / CC1/2: 0.747 / Rpim(I) all: 1.192 / % possible all: 74.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.67→60.26 Å / SU ML: 0.4673 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 599 10.01 %RANDOM
Rwork0.2401 5383 --
obs0.2456 5982 45.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.56 Å2
Refinement stepCycle: LAST / Resolution: 3.67→60.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 852 8 5 5398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415584
X-RAY DIFFRACTIONf_angle_d0.82617759
X-RAY DIFFRACTIONf_chiral_restr0.0521866
X-RAY DIFFRACTIONf_plane_restr0.0078882
X-RAY DIFFRACTIONf_dihedral_angle_d17.16322012
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.838007597484
ens_2d_2CEX-RAY DIFFRACTIONTorsion NCS0.237089090499
ens_3d_2EGX-RAY DIFFRACTIONTorsion NCS0.280099777943
ens_4d_2FHX-RAY DIFFRACTIONTorsion NCS0.507558618118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.67-4.040.2623280.2129257X-RAY DIFFRACTION8.8
4.04-4.630.2924700.2173620X-RAY DIFFRACTION21.37
4.63-5.830.33411610.25371456X-RAY DIFFRACTION49.48
5.83-60.260.27753400.25353050X-RAY DIFFRACTION99.71

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