9CHL | pdb_00009chl

P. vulgaris tetrameric HigBA- operator 2 DNA

• PDB DOI: https://doi.org/10.2210/pdb9CHL/pdb
• NAKB: 9CHL

• 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 government, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.178 (DCC) 

Literature

P. vulgaris tetrameric HigBA- operator 2 DNA

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.98 kDa 
• Atom Count: 8,143 
• Modeled Residue Count: 847 
• Deposited Residue Count: 872 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin HigA	A, C, G [auth E], I [auth G]	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, D, H [auth F], J [auth H]	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')	E [auth I], K	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')	F [auth J], L	21	Proteus vulgaris

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	AA [auth H], N [auth B], P [auth C], R [auth D], W [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	BA [auth K], CA [auth K], DA [auth K], EA [auth L], M [auth A], O [auth B], Q [auth C], S [auth J], T [auth J], U [auth J], V [auth E], X [auth G], Y [auth G], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C, G [auth E], I [auth G]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.178 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.15	α = 90
b = 98.13	β = 109.49
c = 147.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
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 government	United States	--
Other private	United States	--

Revision History  

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