6YL2 | pdb_00006yl2

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/pdb6YL2/pdb
• NAKB: 6YL2

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


• Deposited: 2020-04-06 Released: 2021-04-14 
• Deposition Author(s): Keep, N.H., Pritchard, J.E., Sula, A., Cole, A.R., Kendall, S.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: experimental

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)

Macromolecule Content 

• Total Structure Weight: 54.78 kDa 
• Atom Count: 3,740 
• Modeled Residue Count: 424 
• Deposited Residue Count: 432 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulatory protein (Probably TetR-family)	A [auth B], B [auth A]	196	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*TP*TP*AP*AP*TP*GP*AP*CP*GP*AP*TP*TP*AP*AP*CP*CP*G)-3')	C [auth G]	20	Mycobacterium tuberculosis H37Rv

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*GP*TP*TP*AP*AP*TP*CP*GP*TP*CP*AP*TP*TP*AP*AP*CP*GP*T)-3')	D [auth H]	20	Mycobacterium tuberculosis H37Rv

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.409	α = 90
b = 66	β = 90
c = 179.732	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	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