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- PDB-7cob: Ternary complex of DNA polymerase Mu (Q441A) with 1-nt gapped DNA... -

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Basic information

Entry
Database: PDB / ID: 7cob
TitleTernary complex of DNA polymerase Mu (Q441A) with 1-nt gapped DNA (T:dGMPNPP)
Components
  • DNA (5'-D(*CP*GP*GP*CP*TP*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
KeywordsHYDROLASE/DNA / polymerase mu / misincorporation / gap filling / mutagenesis / HYDROLASE / HYDROLASE-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
Chem-XG4 / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsGuo, M. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670819 China
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of genome instability mediated by human DNA polymerase mu misincorporation.
Authors: Guo, M. / Wang, Y. / Tang, Y. / Chen, Z. / Hou, J. / Dai, J. / Wang, Y. / Wang, L. / Xu, H. / Tian, B. / Hua, Y. / Zhao, Y.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*TP*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)59,4338
Polymers58,8544
Non-polymers5794
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-42 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.760, 68.340, 110.600
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: 53739.113 Da / Num. of mol.: 1 / Mutation: P410G, Q441A, deletion 398-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pET28a / 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*TP*TP*AP*CP*G)-3')


Mass: 2731.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.) 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 / Details: 5' phosphorylated dG / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 241 molecules

#5: Chemical ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 1,4-Dioxane, Tris-HCl, PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.797→29.663 Å / Num. obs: 42776 / % possible obs: 99.7 % / Redundancy: 5.448 % / Biso Wilson estimate: 30.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Χ2: 1.095 / Net I/σ(I): 16.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.845.4650.5762.6316598312830370.8740.63797.1
1.84-1.895.6740.4513.5517307305030500.9220.498100
1.89-1.955.5460.3854.3216350294829480.9360.425100
1.95-2.015.3970.2855.4315631289728960.9610.316100
2.01-2.085.5940.2197.1915686280628040.9820.24399.9
2.08-2.155.6790.1679.2315390271127100.9920.184100
2.15-2.235.5980.13611.1414622261126120.9920.15100
2.23-2.325.2750.11513.0813346253125300.9930.128100
2.32-2.425.6770.08816.1513727241824180.9960.098100
2.42-2.545.6340.07618.6113117232923280.9970.083100
2.54-2.685.4770.06920.8912120221322130.9970.077100
2.68-2.845.2830.05923.9111184211721170.9970.065100
2.84-3.045.5870.0528.2410950196219600.9980.05599.9
3.04-3.285.3980.04331.799948184518430.9980.04899.9
3.28-3.595.0220.03934.928608172217140.9980.04499.5
3.59-4.025.3110.03538.428274156015580.9990.03999.9
4.02-4.645.1160.03338.97071138613820.9980.03799.7
4.64-5.685.1630.03138.56134119111880.9990.03499.7
5.68-8.044.9030.02938.2345559329290.9990.03399.7
8.04-29.6634.5250.02638.724395605390.9990.0396.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.797→29.663 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 2073 4.85 %
Rwork0.1798 40682 -
obs0.1809 42755 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.73 Å2 / Biso mean: 35.0011 Å2 / Biso min: 17 Å2
Refinement stepCycle: final / Resolution: 1.797→29.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 343 34 237 3235
Biso mean--36.53 41.45 -
Num. residues----346
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7974-1.83920.24571380.2387257297
1.8392-1.88520.24491350.22412691100
1.8852-1.93610.22471450.21642682100
1.9361-1.99310.25471480.20362675100
1.9931-2.05740.25171430.19552670100
2.0574-2.13090.22931370.19382697100
2.1309-2.21620.27131000.18592728100
2.2162-2.3170.19551340.19642694100
2.317-2.43910.21541460.19552693100
2.4391-2.59190.22671370.20872723100
2.5919-2.79190.2461480.20562689100
2.7919-3.07250.21181380.20122741100
3.0725-3.51650.20341340.17072756100
3.5165-4.42810.15551460.15052768100
4.4281-29.6630.18861440.1598290399
Refinement TLS params.Method: refined / Origin x: 3.1417 Å / Origin y: 3.5918 Å / Origin z: 11.7977 Å
111213212223313233
T0.2085 Å2-0.0069 Å20.007 Å2-0.2156 Å2-0.0017 Å2--0.2001 Å2
L0.6259 °20.0742 °20.17 °2-0.5154 °20.1291 °2--0.569 °2
S0.0417 Å °-0.0439 Å °-0.0327 Å °0.0118 Å °-0.0389 Å °-0.0026 Å °-0.0064 Å °-0.0069 Å °0 Å °
Refinement TLS groupSelection details: Chain A or Chain T or Chain P or Chain D

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