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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.79 Å
R-Value Free:
0.342 (Depositor), 0.335 (DCC)
R-Value Work:
0.264 (Depositor), 0.268 (DCC)
R-Value Observed:
0.268 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52129
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.79 Å
R-Value Free: 0.342 (Depositor), 0.335 (DCC)
R-Value Work: 0.264 (Depositor), 0.268 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Garcia-Rodriguez, G.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.