8QA9

Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA

• PDB DOI: https://doi.org/10.2210/pdb8QA9/pdb
• NAKB: 8QA9

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-22 Released: 2024-02-21 
• Deposition Author(s): McLean, T.C., Mundy, J.E.A., Lawson, D.M., Le, T.B.K.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.252 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA

McLean, T.C., Mundy, J.E.A., Lawson, D.M., Le, T.B.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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 - B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 87.58 kDa 
• Atom Count: 5,584 
• Modelled Residue Count: 659 
• Deposited Residue Count: 730 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional repressor protein KorB	A, B	237	Escherichia coli	Mutation(s): 0  Gene Names: korB
UniProt
Find proteins for P07674 (Escherichia coli) Explore P07674  Go to UniProtKB:  P07674

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TrfB transcriptional repressor protein	C, D	114	Escherichia coli	Mutation(s): 0  Gene Names: trfB
UniProt
Find proteins for P03052 (Escherichia coli) Explore P03052  Go to UniProtKB:  P03052

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*A)-3')	E, F	14	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.252 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.253	α = 90
b = 77.095	β = 107.42
c = 84.609	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): McLean, T.C., Mundy, J.E.A., Lawson, D.M., Le, T.B.K.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X01097X/1
Wellcome Trust	United Kingdom	221776/Z/20/Z
Royal Society	United Kingdom	URF/R/201020

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release