9FF5 | pdb_00009ff5

The structure of G.kaustophilus T-1 ScoC-23bp dsDNA complex

• PDB DOI: https://doi.org/10.2210/pdb9FF5/pdb
• NAKB: 9FF5

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.282 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

The structure of G.kaustophilus T-1 ScoC-23bp 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: 136.04 kDa 
• Atom Count: 8,400 
• Modeled Residue Count: 833 
• Deposited Residue Count: 951 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator Hpr	C [auth B], D [auth C], E [auth A], F [auth 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: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')	A [auth I], G [auth E], I [auth F]	23	Geobacillus kaustophilus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*TP*TP*GP*TP*TP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')	B [auth J], J [auth H]	23	Geobacillus kaustophilus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*AP*TP*AP*TP*T)-3')	H [auth G]	8	Geobacillus kaustophilus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.282 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.205	α = 90
b = 100.147	β = 112.335
c = 96.606	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	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.

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

Revision History  

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