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- PDB-7m4c: DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex,... -

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Basic information

Entry
Database: PDB / ID: 7m4c
TitleDNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 960 min
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding
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
: / PYROPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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*T)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,09016
Polymers43,3674
Non-polymers72212
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-70 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.021, 62.641, 140.120
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*T)-3')


Mass: 2097.411 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, 251 molecules

#5: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 56.57 % / Mosaicity: 0.197 °
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: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 36795 / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.034 / Rrim(I) all: 0.098 / Χ2: 1.098 / Net I/σ(I): 7.4 / Num. measured all: 323798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.95-1.988.70.96717850.8290.3451.089100
1.98-2.028.80.83518200.890.2951.0911000.886
2.02-2.068.90.68718060.8990.2431.0671000.729
2.06-2.18.90.59318190.930.2091.1211000.629
2.1-2.158.90.52118130.9420.1841.0911000.553
2.15-2.28.90.45417840.9530.1611.1071000.482
2.2-2.258.90.37718560.9720.1331.0951000.401
2.25-2.318.90.33317880.9760.1181.1041000.354
2.31-2.388.90.29218290.9870.1031.1311000.31
2.38-2.468.90.24818230.9840.0881.1231000.263
2.46-2.548.90.20318500.9890.0721.0881000.216
2.54-2.658.90.17618130.9920.0621.0941000.187
2.65-2.778.90.14918140.9940.0531.0671000.158
2.77-2.918.90.12518370.9950.0441.0971000.133
2.91-3.18.80.11118440.9950.041.091000.118
3.1-3.338.80.09718610.9960.0351.2981000.103
3.33-3.678.80.07318530.9970.0261.2071000.077
3.67-4.28.80.05418780.9980.021.0331000.058
4.2-5.298.60.04519120.9980.0161.0521000.048
5.29-508.10.03920100.9980.0150.91899.70.042

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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: 1.95→35.874 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 1799 4.9 %
Rwork0.1813 34926 -
obs0.1828 36725 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.2 Å2 / Biso mean: 42.179 Å2 / Biso min: 18.73 Å2
Refinement stepCycle: final / Resolution: 1.95→35.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 446 33 244 3109
Biso mean--40.98 42.52 -
Num. residues----342
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9501-2.00280.27811320.2291265099
2.0028-2.06180.24751340.21042617100
2.0618-2.12830.24881410.20612606100
2.1283-2.20430.23091340.19292681100
2.2043-2.29260.21771370.18372650100
2.2926-2.39690.22421420.17662672100
2.3969-2.52330.21091370.17432657100
2.5233-2.68130.20831410.17452687100
2.6813-2.88820.22681310.18612666100
2.8882-3.17870.21051440.18522700100
3.1787-3.63830.19031340.17382710100
3.6383-4.58240.19191480.15532743100
4.5824-35.8740.22831440.19512887100
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)
10.3181-0.1475-0.27440.3465-0.01220.3416-0.1085-0.52490.08510.43590.093-0.65470.41430.65430.00070.54230.1609-0.15010.72940.09090.618-7.407-29.41825.313
22.2124-0.0063-0.83481.34220.43141.65090.0925-0.13380.24910.06320.0261-0.0852-0.14380.04320.04530.24250.022-0.02470.2361-0.0380.2752-13.364-6.7219.263
33.0834-0.89630.55361.62040.2660.55610.1937-0.7856-0.25560.54420.0180.08810.04460.25930.16090.5124-0.017-0.01520.6973-0.15440.3857-21.942-4.90131.142
40.01690.01020.00970.07450.02310.0098-0.0212-0.2120.0716-0.05310.1280.3491-0.0045-0.3463-0.00220.50740.00470.040.52950.18720.368-27.912-26.15626.755
50.03610.07260.0160.19590.08990.05790.211-0.1869-0.030.1007-0.03220.18440.0490.10070.00060.28870.0117-0.02550.2332-0.03970.2785-26.654-8.9949.756
60.0568-0.05960.00550.11350.04770.05810.1564-0.1281-0.05450.0155-0.1006-0.1986-0.1756-0.240300.25520.0003-0.01150.255-0.03960.2186-23.344-14.1629.748
70.28240.23770.31550.67480.90031.20750.4471-0.3936-0.19120.56280.1493-0.05590.21640.22970.09270.6719-0.00150.05640.55850.09580.3761-19.384-28.68329.448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 251:320 )A251 - 320
2X-RAY DIFFRACTION2( CHAIN A AND RESID 321:533 )A321 - 533
3X-RAY DIFFRACTION3( CHAIN A AND RESID 534:575 )A534 - 575
4X-RAY DIFFRACTION4( CHAIN T AND RESID 1:4 )T1 - 4
5X-RAY DIFFRACTION5( CHAIN T AND RESID 5:11 )T5 - 11
6X-RAY DIFFRACTION6( CHAIN P AND RESID 1:7 )P1 - 7
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:4 )D1 - 4

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