1MGR | pdb_00001mgr

Crystal structure of RNase Sa3,cytotoxic microbial ribonuclease

• PDB DOI: https://doi.org/10.2210/pdb1MGR/pdb

• Classification: HYDROLASE
• Organism(s): Kitasatospora aureofaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-08-16 Released: 2003-02-04 
• Deposition Author(s): Sevcik, J., Urbanikova, L., Leland, P.A., Raines, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Links X-ray Structure of Two Crystalline Forms of a Streptomycete Ribonuclease with Cytotoxic Activity

Sevcik, J., Urbanikova, L., Leland, P.A., Raines, R.T.

(2002) J Biological Chem 277: 47325-47330

• PubMed: 12228255 
• DOI: https://doi.org/10.1074/jbc.M208425200
• Primary Citation Related Structures: 
  1MGR, 1MGW


• PubMed Abstract: 
  

  Ribonuclease (RNase) Sa3 is secreted by the Gram-positive bacterium Streptomyces aureofaciens. The enzyme catalyzes the cleavage of RNA on the 3' side of guanosine residues. Here, x-ray diffraction analysis was used to determine the three-dimensional structure of two distinct crystalline forms of RNase Sa3 to a resolution of 2.0 and 1.7 A. These two structures are similar to each other as well as to that of a homolog, RNase Sa. All of the key active-site residues of RNase Sa (Asn(42), Glu(44), Glu(57), Arg(72), and His(88)) are located in the putative active site of RNase Sa3. Also herein, RNase Sa3 is shown to be toxic to human erythroleukemia cells in culture. Like onconase, which is an amphibian ribonuclease in Phase III clinical trials as a cancer chemotherapeutic, RNase Sa3 is not inhibited by the cytosolic ribonuclease inhibitor protein. Thus, a prokaryotic ribonuclease can be toxic to mammalian cells.

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Organizational Affiliation: 
• Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84251 Bratislava, Slovak Republic. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.15 kDa 
• Atom Count: 823 
• Modeled Residue Count: 97 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanyl-specific ribonuclease Sa3	A	99	Kitasatospora aureofaciens	Mutation(s): 0  EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P30289 (Kitasatospora aureofaciens) Explore P30289  Go to UniProtKB:  P30289

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.05	α = 90
b = 34.05	β = 90
c = 147.22	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-04 
Deposition Author(s): Sevcik, J., Urbanikova, L., Leland, P.A., Raines, R.T.

Revision History  

• Version 1.0: 2003-02-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary