6Y2S | pdb_00006y2s

Escherichia coli R318A RnlA endoribonuclease (single alanine mutant of RnlA)

• PDB DOI: https://doi.org/10.2210/pdb6Y2S/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2020-02-17 Released: 2021-03-31 
• Deposition Author(s): Garcia-Rodriguez, G., Loris, R.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.79 Å
• R-Value Free: 
  0.342 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: experimental

Literature

Quaternary structure changes control ribonuclease activity of RnlA toxin.

Garcia-Rodriguez, G., Talavera Perez, A., Wilmaerts, D., Michiels, J., Charlier, D., Loris, R.

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: SAXS

Macromolecule Content 

• Total Structure Weight: 83.8 kDa 
• Atom Count: 5,313 
• Modeled Residue Count: 686 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA endoribonuclease toxin LS	A, B	373	Escherichia coli K-12	Mutation(s): 1  Gene Names: rnlA, std, yfjN, b2630, JW2611 EC: 3.1
UniProt
Find proteins for P52129 (Escherichia coli (strain K12)) Explore P52129  Go to UniProtKB:  P52129

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.79 Å
• R-Value Free:  0.342 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.56	α = 90
b = 105.56	β = 90
c = 156.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Garcia-Rodriguez, G., Loris, R.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G.0B25.15N

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description