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- PDB-7m48: DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex,... -

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Basic information

Entry
Database: PDB / ID: 7m48
TitleDNA Polymerase Lambda, TTP:At Mg2+ 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 / DNA Polymerase Lambda / 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
OXALATE ION / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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)43,88215
Polymers43,3674
Non-polymers51511
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-69 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.168, 62.653, 139.912
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: loop1, 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)
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.) synthetic construct (others)
#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.) synthetic construct (others)
#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.) synthetic construct (others)

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Non-polymers , 5 types, 262 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.84 Å3/Da / Density % sol: 56.63 % / Mosaicity: 0.253 °
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 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 37937 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.034 / Rrim(I) all: 0.093 / Χ2: 1.164 / Net I/σ(I): 7.8 / Num. measured all: 281178
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.93-1.967.20.94518860.7930.3721.12699.9
1.96-27.30.75818610.8310.2961.0981000.816
2-2.047.30.68318510.8310.2661.11899.90.735
2.04-2.087.30.54118880.8910.2131.1511000.583
2.08-2.127.40.49918450.9050.1951.1141000.538
2.12-2.177.30.40318800.930.1581.1131000.434
2.17-2.237.40.35318720.9550.1371.1561000.38
2.23-2.297.40.30318810.9620.1181.1241000.326
2.29-2.367.40.2618780.9710.11.1411000.279
2.36-2.437.40.22319020.9760.0871.1631000.24
2.43-2.527.40.19318680.9860.0751.161000.207
2.52-2.627.50.16718850.9890.0641.1931000.179
2.62-2.747.50.14118970.9890.0541.2381000.152
2.74-2.887.50.11718890.9940.0451.1991000.126
2.88-3.067.50.10318970.9930.0391.29199.90.111
3.06-3.37.50.09519160.9920.0361.29499.90.102
3.3-3.637.60.07219050.9960.0271.12999.70.077
3.63-4.167.60.05319400.9980.021.11399.70.057
4.16-5.247.50.04519530.9990.0171.14299.10.048
5.24-507.10.03820430.9990.0141.204980.041

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Processing

Software
NameVersionClassification
PHENIXv1.15.2-3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPQ

3upq


Resolution: 1.93→35.896 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1859 4.91 %
Rwork0.1839 36013 -
obs0.1857 37872 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.36 Å2 / Biso mean: 42.2932 Å2 / Biso min: 17.49 Å2
Refinement stepCycle: final / Resolution: 1.93→35.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 446 28 255 3110
Biso mean--50.83 42.23 -
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 (%)
1.93-1.98220.2981480.2483270299
1.9822-2.04050.28821400.22662748100
2.0405-2.10630.23371430.21122753100
2.1063-2.18160.25411350.20582713100
2.1816-2.26890.21461410.18732737100
2.2689-2.37220.20821420.18272735100
2.3722-2.49720.22071420.18542777100
2.4972-2.65360.20761480.18842743100
2.6536-2.85840.20631380.18822773100
2.8584-3.14590.23521440.18672786100
3.1459-3.60080.2091360.1772784100
3.6008-4.53520.20531550.15472815100
4.5352-35.8960.22071470.1895294799
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)
11.80610.1853-0.61691.62870.04861.4490.0312-0.28780.04060.1760.0398-0.1468-0.02240.1370.00780.20630.0224-0.0460.2849-0.04190.2484-12.0971-12.124313.4326
20-0.0003-0.00010.02040.00570.0016-0.1432-0.0415-0.2036-0.0483-0.1528-0.03170.1207-0.0027-0.00011.21220.2667-0.03190.7015-0.0240.783-35.9016-13.155327.2047
32.6188-0.3753-1.25951.25930.08090.72060.0479-0.65650.0990.4680.095-0.1917-0.39640.6981-0.11910.4416-0.0102-0.040.6303-0.21210.3151-16.498-1.920332.0169
40.284-0.4739-0.13110.83180.23060.0643-0.0264-0.1152-0.2515-0.10770.08860.62070.1422-0.187-0.04710.5097-0.03120.04540.51740.1870.3895-27.8741-26.126426.694
50.13050.0923-0.0060.24820.11760.08120.0937-0.05090.0210.02960.00950.20340.03610.067900.2867-0.00310.00070.2289-0.03250.268-26.0987-9.291512.3314
60.0621-0.06020.00170.065-0.01060.06530.0511-0.2194-0.10290.0668-0.0503-0.0402-0.0641-0.1702-00.24570.01360.00150.2485-0.04330.2187-23.2162-14.16169.7548
70.19880.14350.07341.54550.93510.56670.4253-0.49-0.10690.37390.3258-0.17160.3190.370.2050.5130.00440.03830.54490.06890.3021-19.3871-28.687929.4387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 251 through 538)A251 - 538
2X-RAY DIFFRACTION2(chain 'A' and resid 539 through 548)A539 - 548
3X-RAY DIFFRACTION3(chain 'A' and resid 549 through 575)A549 - 575
4X-RAY DIFFRACTION4(chain 'T' and resid 1 through 4)T1 - 4
5X-RAY DIFFRACTION5(chain 'T' and resid 5 through 11)T5 - 11
6X-RAY DIFFRACTION6(chain 'P' and resid 1 through 7)P1 - 7
7X-RAY DIFFRACTION7(chain 'D' and resid 1 through 4)D1 - 4

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