1CON | pdb_00001con

THE REFINED STRUCTURE OF CADMIUM SUBSTITUTED CONCANAVALIN A AT 2.0 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1CON/pdb

• Classification: LECTIN(AGGLUTININ)
• Organism(s): Canavalia ensiformis
• Mutation(s): No 


• Deposited: 1993-03-16 Released: 1994-01-31 
• Deposition Author(s): Naismith, J.H., Habash, J., Harrop, S.J., Helliwell, J.R., Hunter, W.N., Kalb(Gilboa), A.J., Yariv, J., Wan, T.C.M., Weisgerber, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.171 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Refined structure of cadmium-substituted concanavalin A at 2.0 A resolution.

Naismith, J.H., Habash, J., Harrop, S., Helliwell, J.R., Hunter, W.N., Wan, T.C., Weisgerber, S., Kalb, A.J., Yariv, J.

(1993) Acta Crystallogr D Biol Crystallogr 49: 561-571

• PubMed: 15299493 
• DOI: https://doi.org/10.1107/S0907444993006390
• Primary Citation Related Structures: 
  1CON


• PubMed Abstract: 
  

  The three-dimensional structure of cadmium-substituted concanavalin A has been refined using X-PLOR. The R factor on all data between 8 and 2 A is 17.1%. The protein crystallizes in space group I222 with cell dimensions a = 88.7, b = 86.5 and c = 62.5 A and has one protein subunit per asymmetric unit. The final structure contains 237 amino acids, two Cd ions, one Ca ion and 144 water molecules. One Cd ion occupies the transition-metal binding site and the second occupies an additional site, the coordinates of which were first reported by Weinzierl & Kalb [FEBS Lett. (1971), 18, 268-270]. The additional Cd ion is bound with distorted octahedral symmetry and bridges the cleft between the two monomers which form the conventional dimer of concanavalin A. This study provides a detailed analysis of the refined structure of saccharide-free concanavalin A and is the basis for comparison with saccharide complexes reported elsewhere.

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Organizational Affiliation: 
• Department of Chemistry, University of Manchester, England.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 25.89 kDa 
• Atom Count: 1,956 
• Modeled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CONCANAVALIN A	A	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866  Go to UniProtKB:  P02866

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.171 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.7	α = 90
b = 86.5	β = 90
c = 62.5	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: 1994-01-31 
Deposition Author(s): Naismith, J.H., Habash, J., Harrop, S.J., Helliwell, J.R., Hunter, W.N., Kalb(Gilboa), A.J., Yariv, J., Wan, T.C.M., Weisgerber, S.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other