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- PDB-7m7t: Human DNA Pol eta S113A with dT-ended primer and dATP: in crystal... -

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Basic information

Entry
Database: PDB / ID: 7m7t
TitleHuman DNA Pol eta S113A with dT-ended primer and dATP: in crystallo reaction for 0 s
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*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 / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 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: 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*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5129
Polymers54,6663
Non-polymers8476
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-43 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.629, 98.629, 82.020
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(*AP*GP*CP*GP*TP*CP*AP*T)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 590 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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#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


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
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: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. obs: 77575 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Χ2: 0.991 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.533.10.60635541.023198.2
1.53-1.553.10.49635311.005198.1
1.55-1.583.20.43135211.002198.3
1.58-1.623.20.37435501.01198.5
1.62-1.653.20.33235371.028198.8
1.65-1.693.30.28435851.053198.8
1.69-1.733.30.23935811.016198.8
1.73-1.783.30.20335560.981198.8
1.78-1.833.30.17635481.026199.1
1.83-1.893.30.14235841.014199.4
1.89-1.963.30.11835660.965199.2
1.96-2.043.30.09436050.961199.6
2.04-2.133.30.08235820.891199.6
2.13-2.243.30.07936060.978199.6
2.24-2.383.30.07935840.884199.7
2.38-2.563.30.08636281.022199.8
2.56-2.823.30.07236300.934199.9
2.82-3.233.30.0536050.949199.9
3.23-4.073.30.03236591.102199.9
4.07-303.30.02436530.976198.6

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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: 1.46→26.9 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 5992 7.72 %
Rwork0.1792 71582 -
obs0.1814 77574 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.45 Å2 / Biso mean: 22.7045 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 1.46→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 387 50 584 4386
Biso mean--18.38 31.98 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074189
X-RAY DIFFRACTIONf_angle_d1.0285780
X-RAY DIFFRACTIONf_dihedral_angle_d27.9731682
X-RAY DIFFRACTIONf_chiral_restr0.078640
X-RAY DIFFRACTIONf_plane_restr0.006663
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.46-1.480.34811860.2836229095
1.48-1.490.31081920.2674238298
1.49-1.510.28071950.2561233498
1.51-1.530.29811960.2591233298
1.53-1.550.26841760.2421240298
1.55-1.570.27661880.2288235698
1.57-1.60.24851950.2273236899
1.6-1.620.24152200.2204237699
1.62-1.650.25442100.214236798
1.65-1.670.24811940.2173234599
1.67-1.70.21652090.2065235799
1.7-1.730.23662090.2068241699
1.73-1.770.23632100.198233699
1.77-1.80.22941960.197240199
1.8-1.840.23862070.1938237299
1.84-1.880.24682240.1999234599
1.88-1.930.2351850.188241499
1.93-1.980.23131870.18622412100
1.98-2.040.20932040.18552408100
2.04-2.110.19412020.16812394100
2.11-2.180.20631920.16782395100
2.18-2.270.20692080.16392410100
2.27-2.370.23171770.16942441100
2.37-2.50.21572360.18062349100
2.5-2.650.22052090.18272430100
2.65-2.860.19921960.17952408100
2.86-3.150.18781900.18252442100
3.15-3.60.18741980.14622414100
3.6-4.530.15651870.13522458100

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