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- PDB-9ewe: DNA Polymerase Lambda I493K, E529D, Ca2+ Ground State Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 9ewe
TitleDNA Polymerase Lambda I493K, E529D, 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: 3.04 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
T: DNA template strand
P: DNA primer strand upstream
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2407
Polymers43,1544
Non-polymers863
Water55831
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 area4540 Å2
ΔGint-56 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.801, 62.251, 138.114
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)
#4: 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
#3: 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 , 3 types, 34 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: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM bicine pH7.5 300 mM Na-K tartrate 14% PEG 10K

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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: Dec 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.737→52.25 Å / Num. obs: 8572 / % possible obs: 86.4 % / Redundancy: 9.3 % / CC1/2: 0.975 / Rpim(I) all: 0.204 / Net I/σ(I): 4.6
Reflection shellResolution: 2.737→2.987 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 429 / CC1/2: 0.548 / Rpim(I) all: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→41.55 Å / SU ML: 0.529 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 423 4.96 %RANDOM
Rwork0.2423 8106 --
obs0.2441 8529 86.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.42 Å2
Refinement stepCycle: LAST / Resolution: 3.04→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 426 3 31 2866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022932
X-RAY DIFFRACTIONf_angle_d0.41314055
X-RAY DIFFRACTIONf_chiral_restr0.0365449
X-RAY DIFFRACTIONf_plane_restr0.0032457
X-RAY DIFFRACTIONf_dihedral_angle_d16.26241099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.470.3561000.32741940X-RAY DIFFRACTION63.53
3.47-4.380.30841550.24482956X-RAY DIFFRACTION96.74
4.38-41.550.22891680.20813210X-RAY DIFFRACTION99.85
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)
10.5686693189680.2795923904030.1267177603261.15871870266-0.6194450397761.42231408749-0.3454822792340.54582682810.173051984735-0.564716840331-0.079107515709-0.252613026959-0.5751963772930.581134447696-0.01146064432390.612305799157-0.1440742805630.02596582554580.6165269095950.1346299473940.617890465537-7.6263977236429.9062093362-20.7082527263
21.64633173085-0.8084984390930.1050952457232.397579802840.09482649781190.280130611116-0.0732239808351-0.178796926347-0.2517077566230.2050815800440.2295450640380.08160987521990.2784536542540.0375355459396-0.1742080436780.3089105088050.004350120501340.01928311494040.393799363284-0.03924043550080.313287530554-12.26788638984.17313549879-5.51471413093
30.9405848904920.6216490351670.6933429111511.2967781091-0.6888925818081.96513098524-0.1472186270560.3469878072890.132340008787-0.2994849512140.06617961242890.09537477354350.07287250297250.0139622366350.05555531773780.4193853092350.0371644537046-0.01232460420930.333543738274-0.1357034712710.369916637477-18.66795036354.15476911014-21.9096907092
40.07722875229-0.0709761484055-0.09189526461340.101228241918-0.1274353389251.32143138285-0.110195595426-0.0928645067452-0.03613665439190.0785685895260.1315494624720.08574881887090.001720368297750.1760661305541.277972066120.690378029599-0.199046916672-0.2682457728840.7490504871550.3113579984060.514629291135-19.436779635928.6786866336-29.1720361074
51.21681487111-0.184347320568-0.2832102230152.341207762780.07487970562270.4048356902790.2604506645490.27436862982-0.0742790704435-0.176616185787-0.4503261656760.4985042902050.175390799560.3962675072560.3642049226210.2450745634770.00853603582665-0.05939474711020.394368894174-0.05755311797830.316425761807-26.787509466715.2892175845-17.152348448
62.7364340513-2.768278969681.530149959293.51456635384-0.6896490386681.87723169552-0.12406077838-0.240010534869-0.06608642370930.02587940998210.388892451131-0.1819472117160.5510845602120.2878030390190.1275719284510.2454372558850.1481337865590.1128296866210.4041698947310.05803010304180.296301312355-24.711131686615.0601783209-8.47612456783
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 251 through 340 )AA251 - 3401 - 90
22chain 'A' and (resid 341 through 460 )AA341 - 46091 - 210
33chain 'A' and (resid 461 through 575 )AA461 - 575211 - 320
44chain 'D' and (resid 1 through 4 )DC1 - 4
55chain 'T' and (resid 1 through 11 )TD1 - 11
66chain 'P' and (resid 1 through 6 )PH1 - 6

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