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- PDB-7kt0: DNA Polymerase Mu, dGTP:At Ground State Ternary Complex, 50 mM Mg... -

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Basic information

Entry
Database: PDB / ID: 7kt0
TitleDNA Polymerase Mu, dGTP:At Ground State Ternary Complex, 50 mM Mg2+ (60min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*A)-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


somatic hypermutation of immunoglobulin genes / B cell differentiation / 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: 1.36 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 16, 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*A)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,55717
Polymers45,1784
Non-polymers1,37913
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-47 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.918, 68.568, 110.222
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*A)-3')


Mass: 1190.830 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 , 8 types, 429 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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-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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.51 Å3/Da / Density % sol: 50.92 % / Mosaicity: 0.177 °
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: Aug 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 97735 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.036 / Rrim(I) all: 0.097 / Χ2: 1.068 / Net I/σ(I): 12.2 / Num. measured all: 669543
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.36-1.384.60.78847070.670.40.8891.04498.1
1.38-1.416.40.76548310.780.3280.8351.05899.9
1.41-1.4470.64548390.8530.2630.6981.07299.9
1.44-1.477.20.54248590.8940.2170.5851.105100
1.47-1.57.20.44348650.930.1770.4781.108100
1.5-1.537.20.34748280.9530.1380.3741.136100
1.53-1.577.10.28248610.9640.1140.3051.163100
1.57-1.616.90.23148160.9730.0950.251.16799.9
1.61-1.666.60.18648900.9810.0780.2021.1699.8
1.66-1.716.10.15248450.9850.0660.1661.1899.3
1.71-1.777.40.13848190.9890.0540.1481.116100
1.77-1.857.50.11648930.9920.0450.1251.138100
1.85-1.937.30.09848890.9930.0390.1061.046100
1.93-2.037.20.08748810.9940.0350.0941.06299.9
2.03-2.1670.07749040.9950.0310.0840.95199.8
2.16-2.336.30.07149040.9940.030.0780.94399.7
2.33-2.566.90.07149280.9950.0290.0770.95499.8
2.56-2.937.60.07349650.9950.0280.0781.02899.9
2.93-3.697.20.07949990.9940.0310.0851.01799.6
3.69-506.50.09252120.9820.0380.10.90499.5

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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: 1.36→34.284 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1788 4883 5 %
Rwork0.1613 92759 -
obs0.1622 97642 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.55 Å2 / Biso mean: 24.8486 Å2 / Biso min: 12.09 Å2
Refinement stepCycle: final / Resolution: 1.36→34.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 344 44 431 3383
Biso mean--33.59 34.98 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083295
X-RAY DIFFRACTIONf_angle_d1.0384566
X-RAY DIFFRACTIONf_dihedral_angle_d8.9321798
X-RAY DIFFRACTIONf_chiral_restr0.075494
X-RAY DIFFRACTIONf_plane_restr0.008548
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3604-1.37590.29131510.2913290595
1.3759-1.3920.26771580.2662301999
1.392-1.4090.26341610.23663059100
1.409-1.42690.22281640.21473105100
1.4269-1.44560.24531600.21113023100
1.4456-1.46540.22161620.19863085100
1.4654-1.48640.2281610.19013059100
1.4864-1.50860.2051610.18553072100
1.5086-1.53210.21351630.18253078100
1.5321-1.55730.20841600.17173056100
1.5573-1.58410.19291620.16923073100
1.5841-1.61290.17991620.15783080100
1.6129-1.64390.16811650.15853099100
1.6439-1.67750.17681590.15163048100
1.6775-1.7140.18511640.1596309699
1.714-1.75380.18351600.16143064100
1.7538-1.79770.19161610.1553078100
1.7977-1.84630.1711640.15813092100
1.8463-1.90060.17051630.15023117100
1.9006-1.9620.16841630.15783078100
1.962-2.03210.18931640.15323095100
2.0321-2.11340.17391630.15263100100
2.1134-2.20960.15761640.14753117100
2.2096-2.32610.17411630.14773088100
2.3261-2.47170.15021650.14283123100
2.4717-2.66250.1661640.15493132100
2.6625-2.93030.16721670.16073149100
2.9303-3.35410.15671650.15673151100
3.3541-4.22450.15361690.14673184100
4.2245-34.2840.22241750.1799333499
Refinement TLS params.Method: refined / Origin x: 3.0526 Å / Origin y: -3.7205 Å / Origin z: -11.2719 Å
111213212223313233
T0.1328 Å20.0024 Å2-0.0095 Å2-0.1389 Å20.0045 Å2--0.1135 Å2
L0.857 °2-0.1756 °2-0.164 °2-0.8095 °20.1077 °2--0.646 °2
S0.0278 Å °0.0866 Å °0.0411 Å °-0.0417 Å °-0.018 Å °-0.0318 Å °0.003 Å °0.0182 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA137 - 494
2X-RAY DIFFRACTION1allT1 - 9
3X-RAY DIFFRACTION1allP1 - 4
4X-RAY DIFFRACTION1allD1 - 4
5X-RAY DIFFRACTION1allB1 - 8
6X-RAY DIFFRACTION1allC1
7X-RAY DIFFRACTION1allE1 - 2
8X-RAY DIFFRACTION1allF1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allG1
11X-RAY DIFFRACTION1allH1
12X-RAY DIFFRACTION1allS1 - 486

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