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- PDB-7ksx: DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM M... -

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Basic information

Entry
Database: PDB / ID: 7ksx
TitleDNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (30min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*CP*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


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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / PYROPHOSPHATE / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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*CP*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)46,37214
Polymers45,4834
Non-polymers88910
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-49 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.011, 68.695, 110.522
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 / Mutation: del398-409, P410G
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*CP*TP*AP*CP*G)-3')


Mass: 2716.787 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, 360 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / 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-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / 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.: 350 / 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: 50.89 % / Mosaicity: 0.254 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG4000

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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: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 64263 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.051 / Χ2: 1.039 / Net I/σ(I): 12.6 / Num. measured all: 338599
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.650.84431460.6340.4090.9411.06599.5
1.6-1.635.20.67231920.7390.3210.7471.0499.8
1.63-1.665.10.54631430.830.2610.6071.02899.7
1.66-1.695.10.46931690.860.2270.5231.04299.6
1.69-1.7350.3831850.8980.1850.4231.04799.7
1.73-1.774.90.32231800.9310.1580.3591.06799.7
1.77-1.814.60.24631950.9530.1260.2771.04799.8
1.81-1.864.90.20431800.9670.1010.2281.06199.9
1.86-1.925.50.16831870.9820.0770.1851.07699.9
1.92-1.985.60.13831860.9880.0630.1521.04199.9
1.98-2.055.70.11231910.9920.0510.1231.04899.8
2.05-2.135.70.08532180.9950.0390.0940.98599.9
2.13-2.235.60.07132050.9960.0320.0780.9799.9
2.23-2.355.40.05832130.9970.0270.0640.943100
2.35-2.495.10.04932210.9980.0240.0550.93199.7
2.49-2.6850.04332180.9980.0210.0481.02399.5
2.68-2.955.80.03932510.9980.0180.0431.04899.9
2.95-3.385.70.03332490.9990.0150.0371.03999.2
3.38-4.265.40.02932820.9990.0140.0321.19599.2
4.26-5050.02734520.9980.0140.0311.08899.1

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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: 1.57→41.832 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 3206 4.99 %
Rwork0.1633 60988 -
obs0.1645 64194 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.16 Å2 / Biso mean: 28.8059 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 1.57→41.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 364 31 358 3271
Biso mean--32 38.38 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143214
X-RAY DIFFRACTIONf_angle_d1.2734460
X-RAY DIFFRACTIONf_dihedral_angle_d9.4712411
X-RAY DIFFRACTIONf_chiral_restr0.07489
X-RAY DIFFRACTIONf_plane_restr0.009517
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5701-1.59350.27871280.2482250396
1.5935-1.61840.23391380.22492616100
1.6184-1.6450.26131380.21332623100
1.645-1.67330.241390.2039262499
1.6733-1.70380.23061380.19172630100
1.7038-1.73650.22321370.17632616100
1.7365-1.7720.2081380.17222626100
1.772-1.81050.20081390.16852650100
1.8105-1.85260.20291380.16022624100
1.8526-1.8990.18551380.15452632100
1.899-1.95030.18551380.15772648100
1.9503-2.00770.19881370.16512649100
2.0077-2.07250.19691420.1592647100
2.0725-2.14660.19451390.15532641100
2.1466-2.23250.18021410.15052655100
2.2325-2.33410.16681400.14752661100
2.3341-2.45710.18071390.1422668100
2.4571-2.61110.1741430.15312657100
2.6111-2.81260.17531410.16462667100
2.8126-3.09560.1751390.16972687100
3.0956-3.54330.18821430.1606269499
3.5433-4.46340.15831440.1464270799
4.4634-41.8320.1981490.1807286399
Refinement TLS params.Method: refined / Origin x: 2.9257 Å / Origin y: -4.3422 Å / Origin z: -11.6117 Å
111213212223313233
T0.1852 Å20.0077 Å2-0.0005 Å2-0.1837 Å20.0161 Å2--0.1411 Å2
L1.3572 °2-0.2887 °2-0.149 °2-0.9362 °20.1481 °2--0.7478 °2
S0.0785 Å °0.1207 Å °0.0576 Å °-0.0439 Å °-0.0519 Å °-0.053 Å °0.0289 Å °0.03 Å °0.0018 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA138 - 494
2X-RAY DIFFRACTION1allT1 - 9
3X-RAY DIFFRACTION1allP1 - 5
4X-RAY DIFFRACTION1allD1 - 4
5X-RAY DIFFRACTION1allJ1 - 4
6X-RAY DIFFRACTION1allB1 - 2
7X-RAY DIFFRACTION1allE1
8X-RAY DIFFRACTION1allC1
9X-RAY DIFFRACTION1allF1
10X-RAY DIFFRACTION1allG1
11X-RAY DIFFRACTION1allS1 - 408

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