9CHN | pdb_00009chn

P. vulgaris trimeric HigBA- operator 2 DNA

• PDB DOI: https://doi.org/10.2210/pdb9CHN/pdb
• NAKB: 9CHN

• Classification: ANTITOXIN/DNA BINDING PROTEIN/DNA
• Organism(s): Proteus vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-01 Released: 2025-07-02 
• Deposition Author(s): Pavelich, I.J., Schureck, M.A., Hoffer, E.D., Dunham, C.M.
• Funding Organization(s): Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

P. vulgaris trimeric HigBA- operator 2 DNA

Pavelich, I.J., Schureck, M.A., Hoffer, E.D., Dunham, C.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.16 kDa 
• Atom Count: 3,180 
• Modeled Residue Count: 314 
• Deposited Residue Count: 343 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin HigA	A, C	104	Proteus vulgaris	Mutation(s): 0  Gene Names: higA
UniProt
Find proteins for Q7A224 (Proteus vulgaris) Explore Q7A224  Go to UniProtKB:  Q7A224

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease HigB	B	93	Proteus vulgaris	Mutation(s): 0  Gene Names: higB EC: 3.1
UniProt
Find proteins for Q7A225 (Proteus vulgaris) Explore Q7A225  Go to UniProtKB:  Q7A225

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')	D	21	Proteus vulgaris

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')	E	21	Proteus vulgaris

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	F [auth A], G [auth A], H [auth B], I [auth D], J [auth D], K [auth E], L [auth E], M [auth E], N [auth E], O [auth E], P [auth E], Q [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.82	α = 90
b = 139.82	β = 90
c = 80.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Pavelich, I.J., Schureck, M.A., Hoffer, E.D., Dunham, C.M.

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Funding Organization	Location	Grant Number
Other private	United States	--
Other government	United States	--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release