6YJ2

Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism

• PDB DOI: https://doi.org/10.2210/pdb6YJ2/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-02 Released: 2021-04-14 
• Deposition Author(s): Keep, N.H., Pritchard, J.E., Sula, A., Cole, A.R., Kendall, S.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism

Pritchard, J.E., Sula, A., Cole, A.R., Kendall, S.L., Keep, N.H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.75 kDa 
• Atom Count: 6,044 
• Modelled Residue Count: 755 
• Deposited Residue Count: 860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulatory protein (Probably TetR-family)	A [auth B], B [auth D], C [auth A], D [auth C]	215	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv2506
UniProt
Find proteins for O06169 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O06169  Go to UniProtKB:  O06169

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B], F [auth B], G [auth B], H [auth D], I [auth D], J [auth A], K [auth C], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.764	α = 90
b = 52.874	β = 90.1
c = 91.919	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Keep, N.H., Pritchard, J.E., Sula, A., Cole, A.R., Kendall, S.L.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description