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- PDB-9nkd: Dpo4 DNA polymerase (R332A) in complex with DNA containing an 8ox... -

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Basic information

Entry
Database: PDB / ID: 9nkd
TitleDpo4 DNA polymerase (R332A) in complex with DNA containing an 8oxoG template lesion
Components
  • DNA polymerase IV
  • Primer DNA
  • 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: 2.5 Å
AuthorsPata, J.D. / Liang, B.
Funding support United States, 3items
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
National Science Foundation (NSF, United States)NSF2105167 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: Primer DNA
T: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9946
Polymers49,3683
Non-polymers6263
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-51 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.980, 102.445, 51.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 40171.762 Da / Num. of mol.: 1 / Mutation: R332A
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 , 2 types, 2 molecules PT

#2: DNA chain Primer DNA


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


Mass: 5179.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 22 molecules

#4: 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
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: calcium acetate, HEPES, PEG-3350 / PH range: 6.7-7.6 / 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: 2.5→25 Å / Num. obs: 18784 / % possible obs: 98.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 56.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1831 / CC1/2: 0.746 / Rpim(I) all: 0.32 / Rrim(I) all: 0.697 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000v722data reduction
HKL-2000v722data 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: 2.5→24.74 Å / SU ML: 0.3697 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2798 1854 9.92 %
Rwork0.2105 16842 -
obs0.2176 18696 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 572 32 19 3360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01543457
X-RAY DIFFRACTIONf_angle_d1.44564775
X-RAY DIFFRACTIONf_chiral_restr0.0672542
X-RAY DIFFRACTIONf_plane_restr0.0108502
X-RAY DIFFRACTIONf_dihedral_angle_d22.19751369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.36761360.29181271X-RAY DIFFRACTION98.6
2.57-2.640.35411410.28271251X-RAY DIFFRACTION98.51
2.64-2.730.36721400.27441280X-RAY DIFFRACTION98.82
2.73-2.830.36071460.27161267X-RAY DIFFRACTION99.23
2.83-2.940.34251410.27471294X-RAY DIFFRACTION99.31
2.94-3.070.38991410.25971280X-RAY DIFFRACTION99.65
3.07-3.230.29671460.23191300X-RAY DIFFRACTION99.79
3.23-3.440.29561340.23361291X-RAY DIFFRACTION99.37
3.44-3.70.30741360.21111303X-RAY DIFFRACTION98.29
3.7-4.070.26251440.20941261X-RAY DIFFRACTION96.56
4.07-4.660.25831490.16311314X-RAY DIFFRACTION99.66
4.66-5.850.2171490.19081344X-RAY DIFFRACTION99.53
5.86-24.740.24541510.1841386X-RAY DIFFRACTION97.96

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