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

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Basic information

Entry
Database: PDB / ID: 7coa
TitleTernary complex of DNA polymerase Mu with 1-nt gapped DNA (T:dGMPNPP) and Mn
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


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
: / : / 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: 1.698 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)59,5668
Polymers58,9114
Non-polymers6554
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-28 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.950, 68.570, 110.810
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 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 , 4 types, 365 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 361 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
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: 1.698→28.935 Å / Num. obs: 50943 / % possible obs: 99.5 % / Redundancy: 5.445 % / Biso Wilson estimate: 21.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.065 / Χ2: 0.969 / Net I/σ(I): 17.3
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
1.7-1.744.5030.3793.8716234372636050.8830.42996.8
1.74-1.794.9510.3145.0618135367036630.9430.3599.8
1.79-1.845.6310.2646.4919861352935270.9610.29199.9
1.84-1.95.70.2048.2919676345234520.9780.224100
1.9-1.965.6180.1699.8218656332433210.9820.18699.9
1.96-2.035.4250.13311.7117544323532340.9880.147100
2.03-2.115.7210.10814.1517908313131300.9930.118100
2.11-2.195.7010.08516.6117136300830060.9950.09499.9
2.19-2.295.5080.07418.3516044292329130.9950.08299.7
2.29-2.45.5970.06520.5415413275827540.9960.07199.9
2.4-2.535.7130.05922.8115015263326280.9970.06599.8
2.53-2.685.5890.05524.0913955250524970.9970.06199.7
2.68-2.875.4630.05125.9212919237223650.9970.05699.7
2.87-3.15.6960.04828.6412469219821890.9970.05399.6
3.1-3.45.4870.04830.3211112204020250.9970.05399.3
3.4-3.85.4540.04932.1910079186018480.9960.05499.4
3.8-4.385.5430.0533.759046164016320.9960.05599.5
4.38-5.375.2740.05132.847441141714110.9960.05799.6
5.37-7.595.2310.04632.575822112211130.9970.05199.2
7.59-28.9354.6730.03431.9329446556300.9970.03996.2

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Processing

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

4m04


Resolution: 1.698→28.935 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2585 5.07 %
Rwork0.175 48352 -
obs0.1762 50937 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.07 Å2 / Biso mean: 26.8868 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 1.698→28.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 343 65 361 3386
Biso mean--27.78 36.71 -
Num. residues----345
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6981-1.73070.26861350.2459256096
1.7307-1.76610.26471440.22922663100
1.7661-1.80450.23481340.21182652100
1.8045-1.84640.21911280.20172672100
1.8464-1.89260.22711320.19612681100
1.8926-1.94380.20331410.19562701100
1.9438-2.00090.19941300.19972657100
2.0009-2.06550.23141500.19782676100
2.0655-2.13930.20721490.18692674100
2.1393-2.22490.19261400.18582658100
2.2249-2.32610.17831470.18652675100
2.3261-2.44870.2211440.18632677100
2.4487-2.60210.19111540.18832696100
2.6021-2.80280.23731540.18432672100
2.8028-3.08460.2061470.17862704100
3.0846-3.53020.18261400.1604272599
3.5302-4.44510.16971410.14182762100
4.4451-28.9350.19031750.157284799
Refinement TLS params.Method: refined / Origin x: 3.3111 Å / Origin y: 3.5193 Å / Origin z: 11.6139 Å
111213212223313233
T0.1241 Å2-0.0068 Å20.0024 Å2-0.1322 Å20.0018 Å2--0.1205 Å2
L0.48 °20.0619 °20.1055 °2-0.4409 °20.0114 °2--0.4565 °2
S0.041 Å °-0.0712 Å °-0.0369 Å °0.0278 Å °-0.036 Å °-0.0159 Å °-0 Å °0.0037 Å °-0 Å °
Refinement TLS groupSelection details: Chain A or Chain T or Chain P or Chain D

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