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- PDB-7co9: Ternary complex of DNA polymerase Mu with 1-nt gapped DNA (T:dGMP... -

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Basic information

Entry
Database: PDB / ID: 7co9
TitleTernary complex of DNA polymerase Mu with 1-nt gapped DNA (T:dGMPNPP) and Mg
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: 1.599 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')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5058
Polymers58,9114
Non-polymers5944
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-35 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.080, 68.540, 110.820
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: 53796.164 Da / Num. of mol.: 1 / Mutation: P410G, 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 TDP

#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(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)
#4: 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)

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Non-polymers , 4 types, 383 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.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 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: 1.599→27.513 Å / Num. obs: 60405 / % possible obs: 98.7 % / Redundancy: 5.171 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.044 / Χ2: 1.082 / Net I/σ(I): 22.08
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
1.6-1.643.3540.2643.9713900445541440.9270.31293
1.64-1.694.1870.2285.5617664436842190.9580.26196.6
1.69-1.734.5320.1897.218779423041440.9740.21498
1.73-1.794.9470.1629.0420215413140860.9830.18198.9
1.79-1.855.6090.13611.7322227398239630.990.15199.5
1.85-1.915.6790.10514.8322033388038800.9930.116100
1.91-1.985.5380.0917.2220680373637340.9940.09999.9
1.98-2.065.5340.07220.5819995361836130.9960.0899.9
2.06-2.165.6720.06124.519621346234590.9970.06799.9
2.16-2.265.5640.05427.118327330132940.9970.0699.8
2.26-2.385.4710.04929.3717327317531670.9970.05499.7
2.38-2.535.6660.04432.6316988300229980.9980.04999.9
2.53-2.75.510.04234.3215438281228020.9980.04799.6
2.7-2.925.4370.03836.5514218262926150.9980.04299.5
2.92-3.25.5660.03539.4213486244324230.9980.03999.2
3.2-3.585.2270.03340.711495221821990.9990.03699.1
3.58-4.135.5270.03243.4610784197019510.9990.03599
4.13-5.065.1940.02942.628721169416790.9980.03299.1
5.06-7.155.3910.02943.027014132713010.9980.03298
7.15-27.5134.7140.02641.1634607857340.9990.02993.5

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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: 1.599→27.513 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 3072 5.09 %
Rwork0.1707 57329 -
obs0.172 60401 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.4 Å2 / Biso mean: 26.8194 Å2 / Biso min: 11.08 Å2
Refinement stepCycle: final / Resolution: 1.599→27.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 343 65 379 3412
Biso mean--32.98 37.54 -
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 (%)
1.5991-1.62410.25421370.2142235191
1.6241-1.65070.20611290.1898252896
1.6507-1.67920.21741490.185248396
1.6792-1.70970.25031380.1775254898
1.7097-1.74260.18951520.1775252898
1.7426-1.77810.1751410.1783260299
1.7781-1.81680.21430.1705259699
1.8168-1.8590.19221400.17782598100
1.859-1.90550.17651150.17432640100
1.9055-1.9570.20091350.18242611100
1.957-2.01460.19061360.18192643100
2.0146-2.07960.24641550.1842607100
2.0796-2.15390.20411270.1792628100
2.1539-2.24010.21611540.17732608100
2.2401-2.3420.20781440.18552629100
2.342-2.46540.20381390.17762654100
2.4654-2.61980.21771250.182654100
2.6198-2.82180.19461300.18742642100
2.8218-3.10550.20521360.1826266399
3.1055-3.5540.21431640.1582264199
3.554-4.47460.1481470.1429268099
4.4746-27.5130.18551360.1616279598
Refinement TLS params.Method: refined / Origin x: 3.1677 Å / Origin y: 3.4499 Å / Origin z: 11.4581 Å
111213212223313233
T0.1219 Å2-0.0034 Å20.0063 Å2-0.1291 Å20.0021 Å2--0.1153 Å2
L0.45 °20.0874 °20.1399 °2-0.423 °20.0649 °2--0.4085 °2
S0.0289 Å °-0.0521 Å °-0.0336 Å °0.0127 Å °-0.024 Å °-0.0109 Å °0.0082 Å °0.0036 Å °0 Å °
Refinement TLS groupSelection details: Chain A or Chain T or Chain P or Chain D

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