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- PDB-9nke: Dpo4 DNA polymerase (R336A) in complex with DNA containing an 8ox... -

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Basic information

Entry
Database: PDB / ID: 9nke
TitleDpo4 DNA polymerase (R336A) in complex with DNA containing an 8oxoG template lesion
Components
  • DNA polymerase IV
  • Extended Primer Strand
  • Primer Strand
  • Template DNA
KeywordsTRANSFERASE/DNA / DNA polymerase Translesion synthesis 8oxoG damage / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / 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. ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / 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 / PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPata, J.D. / Liang, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM08057308 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM155805 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Residues in the little finger domain of the Y-family Dpo4 DNA polymerase communicate to restrict synthesis past 8-oxoguanine lesions.
Authors: Disha, S.S. / Punchipatabendi, T.I. / Kaszubowski, J.D. / Liang, B. / Pata, J.D. / Trakselis, M.A.
History
DepositionFeb 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase IV
P: Extended Primer Strand
T: Template DNA
B: DNA polymerase IV
C: Primer Strand
D: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,24612
Polymers99,0496
Non-polymers1,1986
Water1448
1
A: DNA polymerase IV
P: Extended Primer Strand
T: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3477
Polymers49,6813
Non-polymers6664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-64 kcal/mol
Surface area19870 Å2
MethodPISA
2
B: DNA polymerase IV
C: Primer Strand
D: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8995
Polymers49,3683
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-38 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.309, 103.575, 105.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase IV / Pol IV


Mass: 40171.762 Da / Num. of mol.: 2 / Mutation: R336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 3 types, 4 molecules PTDC

#2: DNA chain Extended Primer Strand


Mass: 4329.830 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chain P was extended during crystallization by the addition of dA to the 3' end. The input sequence was: (DG)(DA)(DG)(DC)(DG)(DA)(DT)(DA)(DC)(DC)(DG)(DT)(DG)
Source: (synth.) synthetic construct (others)
#3: DNA chain Template DNA


Mass: 5179.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Primer Strand


Mass: 4016.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 14 molecules

#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: calcium acetate, HEPES, PEG-3350 / PH range: 6.7-7.8 / Temp details: Ambient room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 24064 / % possible obs: 96.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 74.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / Net I/σ(I): 13.9
Reflection shellResolution: 2.9→3.01 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2 / Num. unique obs: 12740 / CC1/2: 0.685 / Rpim(I) all: 0.397 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000v222data reduction
HKL-2000v222data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
Coot0.9.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZ7

3qz7


Resolution: 2.9→24.67 Å / SU ML: 0.4651 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 2017 8.42 %
Rwork0.1975 21944 -
obs0.204 23961 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.47 Å2
Refinement stepCycle: LAST / Resolution: 2.9→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 1209 68 8 6759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01716974
X-RAY DIFFRACTIONf_angle_d1.61539647
X-RAY DIFFRACTIONf_chiral_restr0.06681094
X-RAY DIFFRACTIONf_plane_restr0.0121003
X-RAY DIFFRACTIONf_dihedral_angle_d23.91762782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39531450.30631562X-RAY DIFFRACTION97.71
2.97-3.050.38541480.29871562X-RAY DIFFRACTION98.96
3.05-3.140.35971520.28511574X-RAY DIFFRACTION98.91
3.14-3.240.32121460.26491583X-RAY DIFFRACTION99.31
3.24-3.360.32531280.25371614X-RAY DIFFRACTION99.15
3.36-3.490.31581360.22721550X-RAY DIFFRACTION97.8
3.49-3.650.33121080.23231163X-RAY DIFFRACTION72.09
3.65-3.840.32231430.22941502X-RAY DIFFRACTION94.49
3.85-4.080.27041380.20831608X-RAY DIFFRACTION98.98
4.09-4.40.24851520.15791616X-RAY DIFFRACTION99.66
4.4-4.840.24371530.15211619X-RAY DIFFRACTION99.89
4.84-5.530.24031520.16971637X-RAY DIFFRACTION99.78
5.53-6.940.2881550.19611648X-RAY DIFFRACTION99.94
6.94-24.670.20881610.1591706X-RAY DIFFRACTION98.42

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