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- PDB-7m4i: DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex... -

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Basic information

Entry
Database: PDB / ID: 7m4i
TitleDNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 420 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 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 beta thumb / DNA polymerase, thumb domain superfamily / 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: 2.005 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)43,95014
Polymers43,3524
Non-polymers59810
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-77 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.750, 62.317, 142.177
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, 92 molecules

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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.85 Å3/Da / Density % sol: 56.79 % / Mosaicity: 0.426 °
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: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33609 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.078 / Χ2: 1.144 / Net I/σ(I): 11.2 / Num. measured all: 161791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.80.82315470.7490.4030.9211.09493.8
2.03-2.074.70.6816200.8170.3340.7621.17596.7
2.07-2.114.90.58616260.830.2870.6561.21598.3
2.11-2.154.80.50316580.8510.2520.5661.27199.5
2.15-2.24.90.42316760.8950.210.4741.26199.9
2.2-2.254.90.35116820.9230.1750.3941.309100
2.25-2.314.80.30116920.9430.150.3381.321100
2.31-2.374.90.24916410.9550.1230.2791.247100
2.37-2.444.90.19716910.9710.0970.221.204100
2.44-2.524.90.1716760.9780.0830.191.22399.9
2.52-2.614.90.1416830.9850.0680.1561.107100
2.61-2.714.90.11716750.9910.0570.131.092100
2.71-2.844.90.09916940.9930.0480.111.123100
2.84-2.994.90.08316900.9940.040.0931.062100
2.99-3.174.80.06917040.9960.0320.0771.047100
3.17-3.424.80.06316980.9950.0290.071.02299.9
3.42-3.764.80.0617120.9950.0280.0661.03499.7
3.76-4.314.80.05817260.9950.0270.0641.01699.5
4.31-5.434.80.05917340.9950.0280.0661.07399
5.43-504.40.05617840.9940.0280.0630.9995

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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: 2.005→37.723 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1635 4.87 %
Rwork0.2218 31911 -
obs0.223 33546 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.04 Å2 / Biso mean: 59.4261 Å2 / Biso min: 31.31 Å2
Refinement stepCycle: final / Resolution: 2.005→37.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 445 26 82 2836
Biso mean--52.67 56.27 -
Num. residues----340
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.005-2.06360.34911100.3239237189
2.0636-2.13020.34311430.3104259198
2.1302-2.20640.28521220.29732637100
2.2064-2.29470.31521430.27392658100
2.2947-2.39910.31141430.25752676100
2.3991-2.52560.2821350.25052671100
2.5256-2.68380.32281370.24252663100
2.6838-2.89090.31161340.23932697100
2.8909-3.18170.27891480.24492694100
3.1817-3.64180.22821330.20482728100
3.6418-4.5870.20871480.18132723100
4.587-37.7230.21751390.2172280297
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)
11.42580.045-0.61131.68160.23971.05420.0601-0.17890.07130.24460.0433-0.0567-0.00460.072800.40690.0228-0.0430.4644-0.0560.4479-13.6885-10.465515.3681
20.1221-0.086-0.04960.09360.07510.0801-0.119-0.5636-0.1643-0.3717-0.00450.40070.03260.037400.6829-0.04130.00150.6720.12670.4642-27.0566-22.691726.5008
30.21880.07790.28430.8068-1.0392.04210.384-0.7123-0.0780.90150.98050.6564-1.1509-0.52690.11720.61790.12820.080.6996-0.02180.5247-27.6958-7.978812.0425
40.1279-0.0849-0.06230.21320.01510.09980.1481-0.46540.00690.3141-0.0358-0.3233-0.4645-0.368100.44330.0072-0.01240.5139-0.06420.389-23.9967-14.00319.89
50.22980.040.07630.51330.68260.91020.6529-0.1434-0.23350.59890.3665-0.34770.04950.07180.04740.9186-0.01010.12090.81680.08330.5696-19.5066-28.180530.0471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 252 through 575)A252 - 575
2X-RAY DIFFRACTION2(chain 'T' and resid 1 through 5)T1 - 5
3X-RAY DIFFRACTION3(chain 'T' and resid 6 through 11)T6 - 11
4X-RAY DIFFRACTION4(chain 'P' and resid 1 through 7)P1 - 7
5X-RAY DIFFRACTION5(chain 'D' and resid 1 through 4)D1 - 4

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