2A11 | pdb_00002a11

Crystal Structure of Nuclease Domain of Ribonuclase III from Mycobacterium Tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb2A11/pdb

• Classification: TRANSCRIPTION,TRANSLATION,HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-17 Released: 2005-07-05 
• Deposition Author(s): Akey, D.L., Berger, J.M., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.286 (Depositor) 

Literature

Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A

Akey, D.L., Berger, J.M.

(2005) Protein Sci 14: 2744-2750

• PubMed: 16155207 
• DOI: https://doi.org/10.1110/ps.051665905
• Primary Citation Related Structures: 
  2A11


• PubMed Abstract: 
  

  RNase III enzymes are a highly conserved family of proteins that specifically cleave double-stranded (ds)RNA. These proteins are involved in a diverse group of functions, including ribosomal RNA processing, mRNA maturation and decay, snRNA and snoRNA processing, and RNA interference. Here we report the crystal structure of the nuclease domain of RNase III from the pathogen Mycobacterium tuberculosis. Although globally similar to other RNase III folds, this structure has some features not observed in previously reported models. These include the presence of an additional metal ion near the catalytic site, as well as conserved secondary structural elements that are proposed to have functional roles in the recognition of dsRNAs.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 25.64 kDa 
• Atom Count: 1,321 
• Modeled Residue Count: 154 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease III	A	242	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rnc EC: 3.1.26.3
UniProt
Find proteins for P9WH03 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WH03  Go to UniProtKB:  P9WH03

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.286 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.589	α = 90
b = 72.589	β = 90
c = 96.013	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-05 
Deposition Author(s): Akey, D.L., Berger, J.M., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

Revision History  

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations