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- PDB-7m7s: Human DNA Pol eta S113A with dT-ended primer and 0.1 mM dAMPNPP -

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Basic information

Entry
Database: PDB / ID: 7m7s
TitleHuman DNA Pol eta S113A with dT-ended primer and 0.1 mM dAMPNPP
Components
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA polymerase / Time resolved crystallography / deprotonation / DNA BINDING PROTEIN / TRANSFERASE-DNA complex
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsGregory, M.T. / Gao, Y. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036146 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.
Authors: Gregory, M.T. / Gao, Y. / Cui, Q. / Yang, W.
History
DepositionMar 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 polymerase eta
T: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,36711
Polymers54,9703
Non-polymers1,3978
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-54 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.676, 98.676, 81.832
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 48601.707 Da / Num. of mol.: 1 / Mutation: S113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 399 molecules

#4: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6 / Details: 15% PEG 2000 MME, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. obs: 38744 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Χ2: 1.019 / Net I/σ(I): 9.3 / Num. measured all: 143896
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.883.50.62819251.0251100
1.88-1.923.60.54619321.042199.9
1.92-1.953.60.4719161.0351100
1.95-1.993.60.3519641.0081100
1.99-2.043.70.32819181.0421100
2.04-2.083.70.27619291.0391100
2.08-2.143.70.22719321.0391100
2.14-2.193.70.20219201.0311100
2.19-2.263.70.18219101.054199.9
2.26-2.333.70.16619280.96199.8
2.33-2.413.80.13219451.0231100
2.41-2.513.70.12719350.988199.9
2.51-2.623.80.11619370.9871100
2.62-2.763.80.11119181.0371100
2.76-2.943.80.10619421.0371100
2.94-3.163.80.08419431.0441100
3.16-3.483.80.059194811100
3.48-3.983.80.04819481.024199.9
3.98-5.023.70.03219540.9861100
5.02-353.70.02620000.98199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ecq

4ecq


Resolution: 1.85→31.49 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 2968 7.67 %
Rwork0.1801 35723 -
obs0.1837 38691 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.13 Å2 / Biso mean: 23.4134 Å2 / Biso min: 5 Å2
Refinement stepCycle: final / Resolution: 1.85→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 391 67 391 4203
Biso mean--34.15 29.27 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064143
X-RAY DIFFRACTIONf_angle_d0.8895702
X-RAY DIFFRACTIONf_dihedral_angle_d26.391645
X-RAY DIFFRACTIONf_chiral_restr0.05641
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.880.35621700.286116681838
1.88-1.910.36751240.259517361860
1.91-1.950.31651410.230116811822
1.95-1.980.25771310.196616751806
1.98-2.030.24441450.19316991844
2.03-2.070.24461440.191116851829
2.07-2.120.26541260.195217111837
2.12-2.170.25511480.186617111859
2.17-2.230.23871470.179816861833
2.23-2.290.25151270.189217011828
2.29-2.370.30461280.184117151843
2.37-2.450.23791630.183416621825
2.45-2.550.26621600.203416881848
2.55-2.670.26761410.194317111852
2.67-2.810.24861410.191916821823
2.81-2.980.25361370.202617191856
2.98-3.210.21821290.182917071836
3.21-3.540.20331410.157117141855
3.54-4.050.18971460.143916921838
4.05-5.10.14151280.143717421870
5.1-31.490.20391510.180617381889

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