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- PDB-7m83: Human DNA Pol eta S113A with dA-ended primer and dATP: in crystal... -

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Basic information

Entry
Database: PDB / ID: 7m83
TitleHuman DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction for 0 s
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')
  • DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*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 / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / metal ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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. ...Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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 (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5129
Polymers54,6663
Non-polymers8476
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-47 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.295, 98.295, 81.831
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*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 chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')


Mass: 2435.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 496 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 41.06 %
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, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 62912 / % possible obs: 96.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.056 / Χ2: 1.013 / Net I/σ(I): 15 / Num. measured all: 203083
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.55-1.582.60.58230581.051193.3
1.58-1.612.70.51929911.047193.1
1.61-1.642.60.45229691.049191.7
1.64-1.672.70.38529911.056191.8
1.67-1.712.70.32329431.066191.1
1.71-1.752.70.29329551.091191
1.75-1.792.70.24529821.094191.9
1.79-1.842.80.20630321.099194.2
1.84-1.892.90.17531721.126196.6
1.89-1.953.10.14231661.097198.3
1.95-2.023.30.11532391.045199.7
2.02-2.13.50.09532660.987199.8
2.1-2.23.70.08432501.025199.9
2.2-2.323.70.07932340.975199.9
2.32-2.463.80.07532881.001199.9
2.46-2.653.80.07932530.991199.9
2.65-2.923.80.0732480.812199.9
2.92-3.343.80.0532780.8081100
3.34-4.23.80.03532790.883199.9
4.2-303.70.02533181.214199

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Processing

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

4ecq


Resolution: 1.55→26.81 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 4902 7.8 %
Rwork0.1748 57954 -
obs0.1774 62856 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.89 Å2 / Biso mean: 24.912 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 1.55→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 387 50 491 4286
Biso mean--18.59 32.04 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084132
X-RAY DIFFRACTIONf_angle_d1.1435693
X-RAY DIFFRACTIONf_dihedral_angle_d28.6381674
X-RAY DIFFRACTIONf_chiral_restr0.063634
X-RAY DIFFRACTIONf_plane_restr0.006658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.30881470.26071838198591
1.57-1.590.26411560.24391841199793
1.59-1.60.26741640.241872203694
1.6-1.630.25611730.23541814198793
1.63-1.650.29991580.22931819197791
1.65-1.670.2691550.22321831198691
1.67-1.690.23711610.21621798195991
1.69-1.720.27131400.2131852199291
1.72-1.750.24921690.2161777194691
1.75-1.770.24111620.19841839200192
1.77-1.80.23641530.20051843199693
1.8-1.840.23451700.19951861203194
1.84-1.870.24581860.19861927211396
1.87-1.910.22411460.19051953209998
1.91-1.950.22781640.18771955211998
1.95-20.21531610.17982017217899
2-2.050.24521710.187720072178100
2.05-2.10.20351540.179619982152100
2.1-2.160.23331660.172320062172100
2.16-2.230.20831740.17619942168100
2.23-2.310.2291490.178419902139100
2.31-2.410.22841700.172720322202100
2.41-2.520.20481970.187619572154100
2.52-2.650.21211680.184420112179100
2.65-2.810.2061670.17620062173100
2.81-3.030.19811580.176320122170100
3.03-3.340.19011640.162420142178100
3.34-3.820.18891680.138320052173100
3.82-4.80.15461510.130920512202100
4.81-26.810.17761800.17592034221499

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