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- PDB-7kle: Ternary structure of Dpo4 bound to N7mG in the template base pair... -

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Basic information

Entry
Database: PDB / ID: 7kle
TitleTernary structure of Dpo4 bound to N7mG in the template base paired with incoming dCTP
Components
  • DNA (5'-D(*CP*TP*AP*AP*CP*(FMG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
  • DNA polymerase IV
KeywordsDNA BINDING PROTEIN / DNA polymerase
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
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. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Saccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsKoag, M.-C. / Lee, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES-26676 United States
CitationJournal: To Be Published
Title: Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
Authors: Koag, M.-C. / Lee, S.
History
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase IV
T: DNA (5'-D(*CP*TP*AP*AP*CP*(FMG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4227
Polymers48,8353
Non-polymers5874
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-67 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.650, 102.472, 53.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 39019.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / 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 TP

#2: DNA chain DNA (5'-D(*CP*TP*AP*AP*CP*(FMG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5718.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus P2 (archaea)
#3: DNA chain DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')


Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus P2 (archaea)

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12 to 18% PEG 3350, 100 mM HEPES (pH 6.6), 100 mM calcicum acetate, and 2.5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 11345 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 57.09 Å2 / Rmerge(I) obs: 0.167 / Χ2: 1.021 / Net I/σ(I): 4.5 / Num. measured all: 79435
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.057.20.9915650.4941100
3.05-3.117.30.7725710.5441100
3.11-3.177.30.6285350.5431100
3.17-3.237.30.525590.5681100
3.23-3.37.30.4235640.5921100
3.3-3.387.30.375340.6431100
3.38-3.467.20.325620.6581100
3.46-3.557.20.365730.7751100
3.55-3.665.80.2965381.323199.3
3.66-3.786.80.3135621.7771100
3.78-3.917.20.2345551.0531100
3.91-4.067.10.2165711.0851100
4.06-4.257.10.1545581.2921100
4.25-4.4770.1385861.3911100
4.47-4.7570.1315551.3511100
4.75-5.116.90.125701.1481100
5.11-5.616.80.1125711.0691100
5.61-6.46.90.1045901.0611100
6.4-7.986.90.0845921.3231100
7.98-106.50.0556341.891199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZ7

3qz7


Resolution: 3.003→19.563 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 499 4.77 %
Rwork0.2293 9970 -
obs0.232 10469 92.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.27 Å2 / Biso mean: 54.966 Å2 / Biso min: 19.64 Å2
Refinement stepCycle: final / Resolution: 3.003→19.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 651 31 27 3452
Biso mean--48.78 46.33 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023540
X-RAY DIFFRACTIONf_angle_d0.5694903
X-RAY DIFFRACTIONf_chiral_restr0.041557
X-RAY DIFFRACTIONf_plane_restr0.002505
X-RAY DIFFRACTIONf_dihedral_angle_d18.1632070
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0033-3.30420.39931180.296236089
3.3042-3.77930.36131210.2853223585
3.7793-4.75030.23171440.2131257897
4.7503-100.25361160.1937279799

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