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- PDB-7m8b: Human DNA Pol eta S113A with rA-ended primer and dATP: in crystal... -

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Basic information

Entry
Database: PDB / ID: 7m8b
TitleHuman DNA Pol eta S113A with rA-ended primer and dATP: in crystallo reaction for 140 s
Components
  • DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
  • DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*A)-D(P*A)-3')
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
DIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / 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 29, 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: 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 polymerase eta
T: DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*A)-D(P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,04912
Polymers54,9953
Non-polymers1,0549
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-81 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.707, 98.707, 81.679
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 / DNA chain / DNA/RNA hybrid , 3 types, 3 molecules ATP

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


Mass: 3628.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA/RNA hybrid DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*A)-D(P*A)-3')


Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 488 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
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: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 38394 / % possible obs: 98.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Χ2: 1.02 / Net I/σ(I): 10.9 / Num. measured all: 158226
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.884.10.61118961.009197.7
1.88-1.924.10.50219091.043198
1.92-1.954.10.45418801.052198.3
1.95-1.994.10.33619071.029198.5
1.99-2.044.10.30319131.04198.7
2.04-2.084.10.25218991.035198.9
2.08-2.144.10.21719221.035199
2.14-2.194.10.18619131.021199.3
2.19-2.264.10.16119291.038199.3
2.26-2.334.10.13619250.985199.4
2.33-2.414.10.11519231.038199.7
2.41-2.514.10.1119341.002199.7
2.51-2.624.10.09219231.015199.7
2.62-2.764.10.07819320.998199.9
2.76-2.944.10.06619510.972199.9
2.94-3.164.10.06219380.977199.7
3.16-3.484.20.06419431.001199.4
3.48-3.984.20.05819291.078198.7
3.98-5.024.20.03719110.975198
5.02-404.20.02519171.066195.2

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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→31.46 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 2945 7.68 %
Rwork0.1621 35409 -
obs0.1657 38354 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.15 Å2 / Biso mean: 27.6759 Å2 / Biso min: 5.1 Å2
Refinement stepCycle: final / Resolution: 1.85→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 409 61 479 4314
Biso mean--25.18 33.62 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074185
X-RAY DIFFRACTIONf_angle_d0.9195773
X-RAY DIFFRACTIONf_dihedral_angle_d27.8051682
X-RAY DIFFRACTIONf_chiral_restr0.048639
X-RAY DIFFRACTIONf_plane_restr0.005664
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.880.28481630.2191613177696
1.88-1.910.25511270.20631692181998
1.91-1.940.28261380.20951669180798
1.94-1.980.24531300.18771686181699
1.98-2.020.26571390.18731646178598
2.02-2.070.20251480.17461686183499
2.07-2.110.22761240.16971681180599
2.11-2.170.21491480.16511697184599
2.17-2.230.22611440.15761679182399
2.23-2.290.23631330.161217011834100
2.29-2.370.21611260.164517121838100
2.37-2.450.21491600.166216711831100
2.45-2.550.24111640.176416851849100
2.55-2.660.23821370.174617141851100
2.66-2.80.21071480.170816921840100
2.8-2.980.24141380.170117081846100
2.98-3.210.20991300.167517191849100
3.21-3.530.18261370.14031704184199
3.53-4.040.18081470.13411683183099
4.04-5.090.15071280.13341697182598
5.09-31.460.21361360.17481674181095

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