9QHS | pdb_00009qhs

phiLo family-A DNA polymerase with modified template

PDB DOI: https://doi.org/10.2210/pdb9QHS/pdb
EM Map EMD-52894: EMDB EMDataResource
NAKB: 9QHS

Classification: DNA BINDING PROTEIN
Organism(s): Thermus phage phiLo, DNA molecule
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-03-16 Released: 2026-03-25
Deposition Author(s): Missoury, S., Delarue, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

phiLo family-A DNA polymerase with modified template

Missoury, S., Delarue, M.

To be published.

Macromolecule Content

Total Structure Weight: 151.39 kDa
Atom Count: 10,414
Modeled Residue Count: 1,186
Deposited Residue Count: 1,207
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA-directed DNA polymerase I	A	1,142	Thermus phage phiLo	Mutation(s): 0 Gene Names: phiLo_158

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA template	B [auth T]	35	DNA molecule
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA primer	C [auth P]	30	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCT (Subject of Investigation/LOI) Query on DCT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₂ P₃ ARLKCWCREKRROD-POYBYMJQSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0_5885
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	France	--

Revision History (Full details and data files)

Version 1.0: 2026-03-25
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.