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- PDB-7kt2: DNA Polymerase Mu, dGTP:At Product State Ternary Complex, 50 mM M... -

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Basic information

Entry
Database: PDB / ID: 7kt2
TitleDNA Polymerase Mu, dGTP:At Product State Ternary Complex, 50 mM Mn2+ (225min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION/DNA / time-lapse crystallography / oxidized nucleotide insertion / DNA polymerase mu / double strand break repair / REPLICATION / REPLICATION-DNA complex
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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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 1.0Jan 19, 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 23, 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*AP*TP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*AP*G)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06319
Polymers45,5074
Non-polymers1,55615
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-61 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.893, 68.866, 110.319
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*AP*TP*AP*CP*G)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*G)-3')


Mass: 1520.036 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 , 7 types, 355 molecules

#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.5 Å3/Da / Density % sol: 50.79 % / Mosaicity: 0.184 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG 4000

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. obs: 73665 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Χ2: 1.012 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.535.50.80534950.7870.3620.8860.97197
1.53-1.555.70.72636120.8140.3250.7970.99298.8
1.55-1.585.90.63236240.8540.2790.6921.01499.8
1.58-1.6260.55336480.8820.2440.6061.043100
1.62-1.655.70.43636490.9170.1980.481.01499.8
1.65-1.695.40.35636540.9350.1680.3941.013100
1.69-1.736.30.31136600.9630.1340.3391.034100
1.73-1.786.70.26436430.9750.1090.2861.006100
1.78-1.836.70.20836680.9830.0860.2251.002100
1.83-1.896.60.16936520.9890.070.1831.02100
1.89-1.966.50.13736790.9920.0580.1490.994100
1.96-2.046.40.11136860.9940.0470.1210.99499.9
2.04-2.136.20.08836780.9950.0380.0961.025100
2.13-2.2460.07337100.9960.0320.081100
2.24-2.385.40.0636750.9970.0290.0670.98599.9
2.38-2.566.60.05637090.9970.0230.0610.99799.9
2.56-2.826.80.05237180.9980.0210.0561.008100
2.82-3.236.60.04637460.9980.0190.050.96100
3.23-4.076.10.04138000.9980.0180.0451.08899.9
4.07-505.90.0439590.9960.0180.0441.07399.6

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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: 1.499→34.958 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3677 5 %
Rwork0.1679 69913 -
obs0.1689 73590 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.89 Å2 / Biso mean: 27.2252 Å2 / Biso min: 10.16 Å2
Refinement stepCycle: final / Resolution: 1.499→34.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 366 57 345 3287
Biso mean--28.81 35.62 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013193
X-RAY DIFFRACTIONf_angle_d1.1074425
X-RAY DIFFRACTIONf_dihedral_angle_d17.4551196
X-RAY DIFFRACTIONf_chiral_restr0.078482
X-RAY DIFFRACTIONf_plane_restr0.008504
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4991-1.51880.28261260.2597249994
1.5188-1.53970.26451360.2499261798
1.5397-1.56170.28241390.2283262899
1.5617-1.5850.23751410.21772670100
1.585-1.60970.2321410.21182666100
1.6097-1.63610.22251400.20722672100
1.6361-1.66430.22671420.19252681100
1.6643-1.69460.22251390.19072648100
1.6946-1.72720.20311410.17862681100
1.7272-1.76240.19691410.17122674100
1.7624-1.80080.21291400.17062657100
1.8008-1.84260.17251410.16422674100
1.8426-1.88870.19881410.1612683100
1.8887-1.93980.20911440.17042710100
1.9398-1.99690.17211380.16732662100
1.9969-2.06130.20791430.16142693100
2.0613-2.1350.18821420.16122708100
2.135-2.22040.20081430.15812685100
2.2204-2.32150.17241420.15242697100
2.3215-2.44380.18041420.15352686100
2.4438-2.59690.18041420.15822744100
2.5969-2.79730.19431430.16562704100
2.7973-3.07870.17341440.16812725100
3.0787-3.52380.18321450.1612767100
3.5238-4.43820.15231470.14992768100
4.4382-34.9580.20671540.18272914100
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)
11.7463-0.4483-0.17271.0010.20880.74750.11720.12380.1545-0.0489-0.0694-0.1073-0.01260.03060.01280.14490.00450.01510.13990.02030.10463.393-3.3538-9.8986
20.31350.1366-0.22360.0626-0.09420.15530.19280.4262-0.0136-0.474-0.18350.0114-0.1217-0.13630.00220.30740.0538-0.02630.3637-0.01640.1406-2.9866-6.2709-24.2768
30.00810.01650.01170.00810.010.02220.263-0.03940.0587-0.038-0.10490.17180.2082-0.0374-00.27780.01640.02820.31240.08660.27652.47893.5633-16.5502
40.0748-0.11670.03450.6072-0.4230.34430.02320.1423-0.1057-0.3495-0.03590.18350.3686-0.39760.35090.33580.0194-0.03930.3892-0.13350.16863.2901-22.0235-25.8504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 138 through 494)A138 - 494
2X-RAY DIFFRACTION2(chain 'T' and resid 1 through 9)T1 - 9
3X-RAY DIFFRACTION3(chain 'P' and resid 1 through 5)P1 - 5
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 4)D1 - 4

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