Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 21.00 kDa 
• Atom Count: 1516 
• Residue Count: 184 
• Unique protein chains: 1

4KB4

Crystal structure of ribosome recycling factor mutant R31A from Mycobacterium tuberculosis

• DOI: 10.2210/pdb4KB4/pdb

• Classification: TRANSLATION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-04-23 Released: 2014-03-12 
• Deposition Author(s): Selvaraj, M., Govindan, A., Seshadri, A., Dubey, B., Varshney, U., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.264 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants.

Selvaraj, M., Govindan, A., Seshadri, A., Dubey, B., Varshney, U., Vijayan, M.

(2013) J Biosci 38: 845-855

• PubMed: 24296887 
• DOI: 10.1007/s12038-013-9381-0
• Primary Citation of Related Structures:  
  4KB4, 4KAW, 4KB2, 4KC6, 4KDD


• PubMed Abstract: 
  

Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Crystal structure had revealed higher rigidity of the M. tuberculosis RRF due to the presence of additional salt bridges between domains. Two inter-domain salt bridges and one between the linker region and the domain containing C-terminal residues were disrupted by appropriate mutations. Except for a C-terminal deletion mutant, all mutants showed RRF activity in E. coli when M. tuberculosis EF-G was also co-expressed. The crystal structures of the point mutants, that of the C-terminal deletion mutant and that of the protein grown in the presence of a detergent, were determined. The increased mobility resulting from the disruption of the salt bridge involving the hinge region allows the appropriate mutant to weakly complement E. coli for its deficiency of RRF even in the absence of simultaneous expression of the mycobacterial EF-G. The loss of activity of the C-terminal deletion mutant appears to be partly due to the rigidification of the molecule consequent to changes in the hinge region.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-recycling factor	A	185	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: frr, MT2949, MTCY274.13c, Rv2882c
Find proteins for P9WGY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY1  Go to UniProtKB:  P9WGY1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	A	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.264 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.2	α = 90
b = 40.45	β = 118.41
c = 68.54	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-23 
• Released Date: 2014-03-12 
Deposition Author(s): Selvaraj, M., Govindan, A., Seshadri, A., Dubey, B., Varshney, U., Vijayan, M.

Revision History 

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references