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- PDB-9qhs: phiLo family-A DNA polymerase with modified template -

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Basic information

Entry
Database: PDB / ID: 9qhs
TitlephiLo family-A DNA polymerase with modified template
Components
  • DNA primer
  • DNA template
  • Putative DNA-directed DNA polymerase I
KeywordsDNA BINDING PROTEIN / family-A DNA polymerase / glyscosylase
Function / homology2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciesThermus phage phiLo (virus)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMissoury, S. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
CitationJournal: To Be Published
Title: phiLo family-A DNA polymerase with modified template
Authors: Missoury, S. / Delarue, M.
History
DepositionMar 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA-directed DNA polymerase I
T: DNA template
P: DNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,3915
Polymers150,9153
Non-polymers4752
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Putative DNA-directed DNA polymerase I


Mass: 130874.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage phiLo (virus) / Gene: phiLo_158
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: DNA chain DNA template


Mass: 10693.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA primer


Mass: 9346.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: phiLo family-A DNA polymerase in elongation complex with modified DNA duplex
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.156 MDa / Experimental value: NO
Source (natural)Organism: Thermus phage phiLo (virus)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5885model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70200 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: PDB / Type: experimental model
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410814
ELECTRON MICROSCOPYf_angle_d0.68914909
ELECTRON MICROSCOPYf_dihedral_angle_d19.6311959
ELECTRON MICROSCOPYf_chiral_restr0.0441606
ELECTRON MICROSCOPYf_plane_restr0.0051682

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