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- PDB-7ktb: DNA Polymerase Mu, 8-oxodGTP:Ct Reaction State Ternary Complex, 1... -

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Basic information

Entry
Database: PDB / ID: 7ktb
TitleDNA Polymerase Mu, 8-oxodGTP:Ct Reaction State Ternary Complex, 10 mM Mn2+ (40min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION / Time-Lapse Crystallography / Oxidized Nucleotide Insertion / DNA Polymerase Mu / Double Strand Break Repair
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / 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-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / 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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / PYROPHOSPHATE / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, Japan, 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
Japan Society for the Promotion of Science (JSPS)16K16195 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide.
Authors: Jamsen, J.A. / Sassa, A. / Shock, D.D. / Beard, W.A. / Wilson, S.H.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,42123
Polymers45,4994
Non-polymers1,92119
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-72 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.278, 62.319, 119.130
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-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 40054.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

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DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3')


Mass: 2716.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')


Mass: 1536.036 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 , 8 types, 394 molecules

#5: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#11: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.98 % / Mosaicity: 0.302 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.576→50 Å / Num. obs: 119332 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Χ2: 1.168 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.58-1.615.60.98230770.6430.4551.042100
1.61-1.645.90.85430970.7460.3851.0511000.938
1.64-1.675.90.69830580.8340.3151.0481000.767
1.67-1.75.90.62530880.8650.2821.0691000.687
1.7-1.745.90.51331210.8980.2311.0761000.564
1.74-1.785.90.43430890.9290.1951.0561000.477
1.78-1.825.90.35330850.9440.1581.0781000.387
1.82-1.875.90.27730770.9620.1241.1441000.304
1.87-1.935.90.23231210.9720.1041.1661000.255
1.93-1.995.90.18231050.9810.0821.1921000.2
1.99-2.065.90.14831070.9870.0661.2171000.162
2.06-2.145.90.1231160.9910.0541.2731000.132
2.14-2.245.90.09631350.9930.0431.2781000.105
2.24-2.365.90.07831150.9960.0351.3491000.085
2.36-2.515.90.06131450.9970.0271.2841000.067
2.51-2.75.90.05631360.9970.0251.2141000.062
2.7-2.975.80.05631690.9970.0261.3291000.062
2.97-3.45.90.04231700.9980.0191.0981000.046
3.4-4.295.80.03332210.9990.0151.1161000.037
4.29-505.50.03533760.9970.0171.25999.60.039

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.576→35.038 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 5915 4.96 %
Rwork0.1582 113417 -
obs0.1592 119332 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.76 Å2 / Biso mean: 29.1787 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 1.576→35.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 365 76 382 3352
Biso mean--37.21 40.06 -
Num. residues----343
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.576-1.59380.291870.2879343891
1.5938-1.61250.26661800.26663798100
1.6125-1.63220.24252150.25443796100
1.6322-1.65290.28141910.24723777100
1.6529-1.67460.25711950.24123821100
1.6746-1.69750.23951910.22993755100
1.6975-1.72180.24822080.21553826100
1.7218-1.74750.26432010.20993755100
1.7475-1.77480.20632040.2043854100
1.7748-1.80390.2212070.19273738100
1.8039-1.8350.17161870.17163812100
1.835-1.86840.21242060.16883760100
1.8684-1.90430.19591620.17143818100
1.9043-1.94320.17142080.16293829100
1.9432-1.98540.17081850.15643786100
1.9854-2.03160.19292110.1573750100
2.0316-2.08240.16241870.15943842100
2.0824-2.13870.16811810.15273782100
2.1387-2.20160.17932180.14443794100
2.2016-2.27270.16411980.14493770100
2.2727-2.35390.20962160.13963770100
2.3539-2.44810.1511910.13973816100
2.4481-2.55950.17292030.14433780100
2.5595-2.69440.21691810.15183828100
2.6944-2.86310.16552280.14953767100
2.8631-3.08410.17842000.15043795100
3.0841-3.39420.13542030.13543775100
3.3942-3.88480.1541660.13863828100
3.8848-4.89230.15312160.12983775100
4.8923-35.0380.18911890.1837378299
Refinement TLS params.Method: refined / Origin x: 4.4009 Å / Origin y: -4.6333 Å / Origin z: -13.536 Å
111213212223313233
T0.1811 Å20.0042 Å2-0.0193 Å2-0.199 Å20.0005 Å2--0.1783 Å2
L0.7448 °2-0.0489 °2-0.2116 °2-1.0692 °20.3508 °2--1.0287 °2
S0.0195 Å °0.0267 Å °-0.0375 Å °0.0142 Å °-0.0322 Å °-0.051 Å °-0.0274 Å °0.056 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA138 - 494
2X-RAY DIFFRACTION1allT1 - 9
3X-RAY DIFFRACTION1allP1 - 5
4X-RAY DIFFRACTION1allD1 - 4
5X-RAY DIFFRACTION1allB1
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allF1 - 9
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1 - 6
10X-RAY DIFFRACTION1allJ1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allS2 - 420

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