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- PDB-7m4g: DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex... -

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Basic information

Entry
Database: PDB / ID: 7m4g
TitleDNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 960 min
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*CP*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
KeywordsREPLICATION / Time-Lapse Crystallography / Double Strand Break Repair / DNA Synthesis Fidelity
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
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050161 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1K99ES029572-01 United States
CitationJournal: Nat Commun / Year: 2022
Title: Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints.
Authors: Jamsen, J.A. / Shock, D.D. / Wilson, S.H.
History
DepositionMar 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
T: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*AP*CP*C)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,78913
Polymers43,3524
Non-polymers4379
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-79 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.997, 62.235, 141.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 36703.977 Da / Num. of mol.: 1 / Mutation: C543A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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 TPD

#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*CP*C)-3')


Mass: 2082.400 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, 150 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.6 % / Mosaicity: 0.332 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 40938 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Rrim(I) all: 0.055 / Χ2: 1.075 / Net I/σ(I): 13.5 / Num. measured all: 239319
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.915.50.82619820.830.380.9111.14499.3
1.91-1.955.60.6320390.8950.2890.6941.14699.3
1.95-1.985.60.53219800.9270.2430.5861.1599.3
1.98-2.035.60.44120120.930.2010.4851.16499.6
2.03-2.075.60.31620210.9640.1440.3481.16699.6
2.07-2.125.70.26919860.9730.1230.2961.1799.7
2.12-2.175.70.21220440.9820.0970.2341.181100
2.17-2.235.80.17820270.9870.080.1961.129100
2.23-2.295.80.15220140.990.0690.1671.084100
2.29-2.375.90.12120220.9930.0550.1331.013100
2.37-2.455.90.09720590.9950.0430.1070.946100
2.45-2.5560.08320320.9970.0370.0910.961100
2.55-2.6760.07620400.9960.0340.0831.01100
2.67-2.816.10.07220580.9960.0320.0791.075100
2.81-2.986.10.07520600.9950.0330.0821.089100
2.98-3.216.10.07720480.9920.0340.0841.031100
3.21-3.546.10.06620640.9930.030.0730.966100
3.54-4.056.10.04220920.9980.0190.0461.002100
4.05-5.160.03221230.9990.0140.0351.11100
5.1-505.60.03322350.9970.0160.0371.02599.5

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Processing

Software
NameVersionClassification
PHENIXv1.15.2-3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPQ

3upq


Resolution: 1.88→39.926 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 2003 4.9 %
Rwork0.2115 38843 -
obs0.2129 40846 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.82 Å2 / Biso mean: 55.727 Å2 / Biso min: 30.05 Å2
Refinement stepCycle: final / Resolution: 1.88→39.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 445 22 146 2892
Biso mean--64.05 52.78 -
Num. residues----332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.92650.36271390.3046268698
1.9265-1.97860.34781440.277269199
1.9786-2.03680.29311390.2683273199
2.0368-2.10260.26231430.2345273499
2.1026-2.17770.25291310.23712741100
2.1777-2.26490.29331460.22582770100
2.2649-2.3680.28251460.23422730100
2.368-2.49280.29191370.22822782100
2.4928-2.64890.28241500.22622770100
2.6489-2.85340.26431400.22932779100
2.8534-3.14050.26411480.23032791100
3.1405-3.59460.21121350.20132821100
3.5946-4.52790.21851530.17762826100
4.5279-39.9260.20971520.20762991100
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)
12.12490.272-0.7931.82970.27351.61210.0863-0.23370.12370.21720.0817-0.1074-0.01440.14450.00130.33650.029-0.05160.4166-0.08510.4058-13.201-10.86115.113
20.1747-0.0364-0.17650.05210.11740.36760.0651-0.39890.10580.36630.3680.4019-0.4518-0.9256-0.00270.59830.04170.01220.63680.02590.4793-27.6526-12.723916.5026
30.1534-0.0494-0.06930.2382-0.10710.1710.1006-0.4221-0.12190.4254-0.058-0.1026-0.5474-0.2053-0.00080.49090.0246-0.01930.4354-0.05660.3561-24.1251-13.8959.7973
40.09390.01460.03580.0964-0.02630.12440.2767-0.0609-0.36220.39920.0339-0.39010.34690.22240.00040.7925-0.0160.12060.75570.09910.5569-19.7128-28.01730.0176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 251 through 575)A251 - 575
2X-RAY DIFFRACTION2(chain 'T' and resid 1 through 11)T1 - 11
3X-RAY DIFFRACTION3(chain 'P' and resid 1 through 7)P1 - 7
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 4)D1 - 4

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