Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.43 kDa 
• Atom Count: 4440 
• Residue Count: 529 
• Unique protein chains: 2

2AAI

Crystallographic refinement of ricin to 2.5 Angstroms

• DOI: 10.2210/pdb2AAI/pdb

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


• Deposited: 1993-09-07 Released: 1994-01-31 
• Deposition Author(s): Rutenber, E., Katzin, B.J., Montfort, W., Villafranca, J.E., Ernst, S.R., Collins, E.J., Mlsna, D., Monzingo, A.F., Ready, M.P., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Crystallographic refinement of ricin to 2.5 A.

Rutenber, E., Katzin, B.J., Ernst, S., Collins, E.J., Mlsna, D., Ready, M.P., Robertus, J.D.

(1991) Proteins 10: 240-250

• PubMed: 1881880 
• DOI: 10.1002/prot.340100308
• Primary Citation of Related Structures:  
  2AAI


• PubMed Abstract: 
  

The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 A and 4.67 degrees, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 A. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.

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Related Citations: 

• Structure of Ricin A-Chain at 2.5 Angstroms
  Katzin, B.J., Collins, E.J., Robertus, J.D.
  (1991) Proteins 10: 251

• Structure of Ricin B-Chain at 2.5 Angstroms
  Rutenber, E., Robertus, J.D.
  (1991) Proteins 10: 260

• The Three-Dimensional Structure of Ricin at 2.8 Angstroms
  Montfort, W., Villafranca, J.E., Monzingo, A.F., Ernst, S.R., Katzin, B., Rutenber, E., Xuong, N.H., Hamlin, R., Robertus, J.D.
  (1987) J Biol Chem 262: 5398

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Organizational Affiliation: 

Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin 78712.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RICIN (A CHAIN)	A	267	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RICIN (B CHAIN)	B	262	N/A	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	5		N-Glycosylation

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	C, D	beta-lactose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.74	α = 90
b = 78.49	β = 90
c = 114.34	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-09-07 
• Released Date: 1994-01-31 
Deposition Author(s): Rutenber, E., Katzin, B.J., Montfort, W., Villafranca, J.E., Ernst, S.R., Collins, E.J., Mlsna, D., Monzingo, A.F., Ready, M.P., Robertus, J.D.

Revision History 

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2013-08-14
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary