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- PDB-9ewd: DNA Polymerase Lambda I493K E529D, TMP:At Ca2+ Ground State Terna... -

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Basic information

Entry
Database: PDB / ID: 9ewd
TitleDNA Polymerase Lambda I493K E529D, TMP: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: 2.12 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 (5'P)
P: DNA primer strand upstream
T: DNA template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,91914
Polymers43,1544
Non-polymers76510
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, DNA polymerase activity assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-55 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.400, 62.470, 139.570
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 (5'P)


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: 36795.086 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 , 7 types, 220 molecules

#5: 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
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM bicine pH7.5 300 mM Na-K tartrate 20% PEG 20K

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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: Sep 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.12→46.55 Å / Num. obs: 28562 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.99 / Rpim(I) all: 0.038 / Net I/σ(I): 16.6
Reflection shellResolution: 2.12→2.18 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4503 / CC1/2: 0.794 / Rpim(I) all: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→35.89 Å / SU ML: 0.3287 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1426 5 %RANDOM
Rwork0.2015 27113 --
obs0.2037 28539 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.42 Å2
Refinement stepCycle: LAST / Resolution: 2.12→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 426 44 210 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813046
X-RAY DIFFRACTIONf_angle_d0.9254200
X-RAY DIFFRACTIONf_chiral_restr0.0523465
X-RAY DIFFRACTIONf_plane_restr0.0094466
X-RAY DIFFRACTIONf_dihedral_angle_d20.14291191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.20.39891370.36412601X-RAY DIFFRACTION98.03
2.2-2.290.33411410.29822693X-RAY DIFFRACTION100
2.29-2.390.33781410.25972668X-RAY DIFFRACTION99.96
2.39-2.520.28511400.23232668X-RAY DIFFRACTION99.93
2.52-2.680.26921430.22542703X-RAY DIFFRACTION99.96
2.68-2.880.32491410.24642691X-RAY DIFFRACTION99.96
2.88-3.170.2721430.2172714X-RAY DIFFRACTION99.97
3.17-3.630.26321430.19412708X-RAY DIFFRACTION99.93
3.63-4.570.20331460.16542772X-RAY DIFFRACTION100
4.57-35.890.1891510.17292895X-RAY DIFFRACTION99.8

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