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- PDB-6vf1: DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50... -

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Basic information

Entry
Database: PDB / ID: 6vf1
TitleDNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mg2+ (120 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: 1.68 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 Mg2+ (120 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)46,20013
Polymers45,5394
Non-polymers6619
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-56 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.044, 68.415, 111.070
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 , 8 types, 371 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: 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
#9: 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
#10: 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
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.5 Å3/Da / Density % sol: 50.89 % / Mosaicity: 0.358 °
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: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 52575 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.038 / Rrim(I) all: 0.084 / Χ2: 1.085 / Net I/σ(I): 14.6 / Num. measured all: 242380
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.714.30.99626160.5330.5181.1271.14299.5
1.71-1.744.70.86425920.7150.4180.9621.146100
1.74-1.774.80.76326200.7730.3680.8491.14999.9
1.77-1.814.80.6125930.8370.2930.6791.153100
1.81-1.854.80.50126120.8720.2430.5591.129100
1.85-1.894.70.426020.910.1950.4461.15799.6
1.89-1.944.70.33426280.940.1630.3731.16199.7
1.94-1.994.70.2625810.9590.1280.291.16799.5
1.99-2.054.70.21325820.9730.1050.2381.1598.5
2.05-2.124.60.16625950.980.0830.1871.12198.7
2.12-2.194.50.12925730.9870.0660.1461.09298.9
2.19-2.284.30.10426210.990.0550.1181.06998.8
2.28-2.383.90.0825840.9920.0450.0931.02897.8
2.38-2.514.90.07126270.9950.0350.080.91199.7
2.51-2.674.90.06226560.9960.0310.070.975100
2.67-2.874.80.05726610.9960.0280.0641.02899.9
2.87-3.164.80.04826520.9970.0250.0541.09199.5
3.16-3.624.60.0426790.9970.0210.0461.01199.6
3.62-4.564.10.03326340.9980.0180.0380.96796.8
4.56-504.60.03228670.9980.0160.0361.05899.8

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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: 1.68→35.023 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 2623 5 %
Rwork0.1625 49884 -
obs0.1638 52507 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.27 Å2 / Biso mean: 23.8084 Å2 / Biso min: 8.74 Å2
Refinement stepCycle: final / Resolution: 1.68→35.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 368 19 370 3312
Biso mean--38.21 34.62 -
Num. residues----348
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.68-1.71020.26491330.2299256497
1.7102-1.74310.25321360.21182575100
1.7431-1.77870.2331370.2022609100
1.7787-1.81740.21351380.18692625100
1.8174-1.85970.21951390.1832619100
1.8597-1.90620.21291400.17232582100
1.9062-1.95770.19761290.17552611100
1.9577-2.01530.20131380.1669262199
2.0153-2.08030.20521340.1612257099
2.0803-2.15470.21251390.1569259199
2.1547-2.24090.17711370.1463260999
2.2409-2.34290.1821350.1477258798
2.3429-2.46640.1731390.1439261599
2.4664-2.62090.18361380.15362655100
2.6209-2.82320.19751380.16312651100
2.8232-3.10710.18741420.1663265899
3.1071-3.55630.17171400.15392661100
3.5563-4.47910.13881400.1403263297
4.4791-35.0230.20521510.17942849100
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)
10.9219-0.1497-0.17860.86190.13480.65910.04670.07580.0572-0.0176-0.0348-0.049-0.00410.02440.00360.10650.0069-0.00830.110.0130.08393.6464-3.1621-9.8932
20.22410.11770.00470.0686-0.03740.22620.10170.1961-0.0144-0.2801-0.11610.023-0.0685-0.1163-0.00870.21540.0169-0.01810.218-0.01950.0904-2.9998-6.1345-24.263
30.0218-0.0180.01870.0354-0.01890.02550.0907-0.1929-0.1240.1073-0.04260.09040.2383-0.0589-0.00150.2528-0.0143-0.00530.21980.04030.13482.73523.5284-16.3605
40.0334-0.05130.02080.1421-0.08130.05150.0347-0.0305-0.1347-0.1197-0.00220.03730.2568-0.09010.09190.245-0.0021-0.02790.2543-0.07040.14523.342-21.9746-26.0827
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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