1RTC | pdb_00001rtc

THE STRUCTURE OF RECOMBINANT RICIN A CHAIN AT 2.3 ANGSTROMS

• PDB DOI: https://doi.org/10.2210/pdb1RTC/pdb

• Classification: GLYCOSIDASE
• Organism(s): Ricinus communis
• Mutation(s): No 


• Deposited: 1992-10-29 Released: 1993-10-31 
• Deposition Author(s): Mlsna, D., Monzingo, A.F., Katzin, B.J., Ernst, S., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structure of recombinant ricin A chain at 2.3 A.

Mlsna, D., Monzingo, A.F., Katzin, B.J., Ernst, S., Robertus, J.D.

(1993) Protein Sci 2: 429-435

• PubMed: 8453380 
• DOI: https://doi.org/10.1002/pro.5560020315
• Primary Citation Related Structures: 
  1RTC


• PubMed Abstract: 
  

  The plant cytotoxin ricin is a heterodimer with a cell surface binding (B) chain and an enzymatically active A chain (RTA) known to act as a specific N-glycosidase. RTA must be separated from B chain to attack rRNA. The X-ray structure of ricin has been solved recently; here we report the structure of the isolated A chain expressed from a clone in Escherichia coli. This structure of wild-type rRTA has and will continue to serve as the parent compound for difference Fouriers used to assess the structure of site-directed mutants designed to analyze the mechanism of this medically and commercially important toxin. The structure of the recombinant protein, rRTA, is virtually identical to that seen previously for A chain in the heterodimeric toxin. Some minor conformational changes due to interactions with B chain and to crystal packing differences are described. Perhaps the most significant difference is the presence in rRTA of an additional active site water. This molecule is positioned to act as the ultimate nucleophile in the depurination reaction mechanism proposed by Monzingo and Robertus (1992, J. Mol. Biol. 227, 1136-1145).

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Texas, Austin 78712.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.07 kDa 
• Atom Count: 2,180 
• Modeled Residue Count: 268 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RICIN	A	268	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.6	α = 90
b = 68.1	β = 112.9
c = 50.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Mlsna, D., Monzingo, A.F., Katzin, B.J., Ernst, S., Robertus, J.D.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Other