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- PDB-6vf6: DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50... -

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Basic information

Entry
Database: PDB / ID: 6vf6
TitleDNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mn2+ (960 min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*(8GM))-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION / Time-Lapse Crystallography / Oxidized Ribonucleotide Insertion / DNA Polymerase Mu / Double Strand Break Repair
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 / nucleus / metal ion binding
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 / GLYCOLIC ACID / : / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, Japan, 4items
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)Z01-10ES050161 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1K99ES029572-01 United States
Japan Society for the Promotion of Science (JSPS)16K16195 Japan
CitationJournal: To be published
Title: DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mn2+ (960 min)
Authors: Jamsen, J.A. / Sassa, A. / Shock, D.D. / Beard, W.A. / Wilson, S.H.
History
DepositionJan 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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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*AP*(8GM))-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,59418
Polymers45,5394
Non-polymers1,05514
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-57 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.263, 62.333, 118.847
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.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*(8GM))-3')


Mass: 1552.035 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 / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 315 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / 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-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
#10: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.45 Å3/Da / Density % sol: 49.81 % / Mosaicity: 0.293 °
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: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 50793 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Χ2: 1.006 / Net I/σ(I): 10.1 / Num. measured all: 331237
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.69-1.725.90.99324740.6140.4441.0920.95199.8
1.72-1.755.70.86524970.6870.3890.9520.97799.5
1.75-1.786.20.76525000.7310.3330.8371.00199.6
1.78-1.826.90.64825230.8280.2690.7030.978100
1.82-1.8670.52925060.870.2170.5731.01699.9
1.86-1.970.46124840.8950.1910.51.049100
1.9-1.956.70.37625330.9220.1590.4091.13199.7
1.95-26.90.29325240.9570.1220.3181.06199.9
2-2.066.70.23825020.970.1010.2591.04199.8
2.06-2.136.60.19425170.9780.0820.2111.04399.8
2.13-2.216.60.15625150.9860.0660.170.985100
2.21-2.296.20.1325480.9890.0570.1421.07899.8
2.29-2.45.80.10425330.9910.0470.1151.0199.8
2.4-2.525.80.0925300.9930.040.0980.9999.6
2.52-2.687.10.0825340.9940.0320.0871.02199.9
2.68-2.897.10.06825710.9970.0270.0740.99299.9
2.89-3.1870.05825660.9970.0240.0630.97599.9
3.18-3.646.70.05125710.9970.0210.0550.90699.8
3.64-4.595.80.04726190.9960.0210.0520.9199.5
4.59-506.40.05227460.9950.0220.0560.98899.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.69→33.435 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 2542 5.01 %
Rwork0.1655 48184 -
obs0.1667 50726 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.9 Å2 / Biso mean: 29.5815 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.69→33.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 368 28 307 3211
Biso mean--44.73 38.24 -
Num. residues----344
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.69-1.72250.28881300.2379259697
1.7225-1.75770.22331540.2147258699
1.7577-1.79590.22611400.20262628100
1.7959-1.83760.26131390.18352680100
1.8376-1.88360.23061330.17332683100
1.8836-1.93450.2071510.17722607100
1.9345-1.99140.18651300.16252647100
1.9914-2.05570.18571310.16622659100
2.0557-2.12920.15761320.1652690100
2.1292-2.21440.17831540.15382649100
2.2144-2.31520.1711330.14822683100
2.3152-2.43720.1631510.14982645100
2.4372-2.58980.19751350.15872699100
2.5898-2.78970.211440.16652677100
2.7897-3.07030.19041540.16872696100
3.0703-3.51410.18941410.15972737100
3.5141-4.42580.15311360.14292750100
4.4258-33.4350.20481540.1855287299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3078-0.1717-0.2871.17130.46051.13890.02280.0076-0.08170.0816-0.0297-0.06-0.01150.08170.00060.16870.0069-0.02580.18930.00860.16414.9884-4.3605-11.505
20.14320.1115-0.04580.1377-0.11650.13770.17260.118-0.055-0.553-0.16510.1453-0.2961-0.23050.00070.28610.027-0.03180.2237-0.03560.1838-2.2612-6.499-25.7096
30.05620.007-0.00210.02880.02660.02540.10240.0038-0.17890.015-0.05810.11490.1691-0.0287-00.2816-0.0087-0.01290.2550.00430.19682.99832.5744-17.482
40.1518-0.12220.18360.1133-0.16160.2336-0.0341-0.1389-0.1732-0.13420.1801-0.07460.1861-0.19420.01260.26220.0112-0.01950.3182-0.07210.24786.571-20.1167-29.4769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 137 through 494)A137 - 494
2X-RAY DIFFRACTION2(chain 'T' and resid 1 through 9)T1 - 9
3X-RAY DIFFRACTION3(chain 'P' and resid 1 through 5)P1 - 5
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 4)D1 - 4

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