9B15 | pdb_00009b15

Superfamily 2 helicase Hel308 containing the beta-hairpin from DNA pol theta helicase-like domain

PDB DOI: https://doi.org/10.2210/pdb9B15/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-13 Released: 2025-03-19
Deposition Author(s): Eckenroth, B.E., Doublie, S.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.221 (Depositor), 0.223 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The stunted beta-hairpin motif and helix-hairpin-helix subdomain 5 modulate the DNA-dependent activities of polymerase theta helicase-like domain

Vanson, S., Eckenroth, B.E., Moharana, K., McBride, M., Averill, A.M., Doublie, S.

To be published.

Macromolecule Content

Total Structure Weight: 158.17 kDa
Atom Count: 11,057
Modeled Residue Count: 1,362
Deposited Residue Count: 1,398
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase Hel308	A, B	699	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: hel308, AF_2245 EC: 5.6.2.4
UniProt
Find proteins for P0DMI1 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore P0DMI1 Go to UniProtKB: P0DMI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DMI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.221 (Depositor), 0.223 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.199	α = 90
b = 174.128	β = 90
c = 85.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Eckenroth, B.E.

Doublie, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA247773
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA233185