9FF4 | pdb_00009ff4

The structure of G.kaustophilus T-1 ScoC-17bp dsDNA complex

• PDB DOI: https://doi.org/10.2210/pdb9FF4/pdb
• NAKB: 9FF4

• Classification: DNA BINDING PROTEIN
• Organism(s): Geobacillus kaustophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-22 Released: 2025-06-04 
• Deposition Author(s): Hadad, N., Shulami, S., Pomyalov, S., Shoham, Y., Shoham, G.
• Funding Organization(s): Israel Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.293 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

The structure of G.kaustophilus T-1 ScoC-17bp dsDNA complex

Hadad, N., Shulami, S., Pomyalov, S., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 143.62 kDa 
• Atom Count: 8,911 
• Modeled Residue Count: 852 
• Deposited Residue Count: 972 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator Hpr	A [auth B], B [auth C], C [auth A], D	207	Geobacillus kaustophilus	Mutation(s): 0  Gene Names: hpr, GK0652
UniProt
Find proteins for Q5L293 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L293  Go to UniProtKB:  Q5L293

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-3')	E [auth H], G [auth M], I [auth G], K	18	Geobacillus kaustophilus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')	F [auth L], H [auth F], J, L [auth N]	18	Geobacillus kaustophilus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	M [auth B], O [auth C], P [auth A], R [auth D]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
MG	N [auth B], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.293 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.634	α = 89.773
b = 70.546	β = 81.625
c = 95.468	γ = 60.911

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Hadad, N., Shulami, S., Pomyalov, S., Shoham, Y., Shoham, G.

---

Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	500/10

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release