1JBC | pdb_00001jbc

CONCANAVALIN A

• PDB DOI: https://doi.org/10.2210/pdb1JBC/pdb

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


• Deposited: 1996-08-23 Released: 1997-02-12 
• Deposition Author(s): Parkin, S., Rupp, B., Hope, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.167 (Depositor) 
• R-Value Work: 
  0.175 (DCC) 

Starting Model: experimental

Literature

Atomic resolution structure of concanavalin A at 120 K.

Parkin, S., Rupp, B., Hope, H.

(1996) Acta Crystallogr D Biol Crystallogr 52: 1161-1168

• PubMed: 15299577 
• DOI: https://doi.org/10.1107/S0907444996009237
• Primary Citation Related Structures: 
  1JBC


• PubMed Abstract: 
  

  The structure of native concanavalin A has been refined to a resolution of 1.2 A against data collected at 120 K. The space group is I222, with a = 61.954 (8), b = 86.053 (11), c = 89.079 (11) A. The structure was refined by restrained weighted least-squares minimization of sum w(F(o)(2) - F(c)(2)(2) with SHELXL92/3/6. The final model contains all of the atoms from 237 amino acids, two metal ions and 271 water molecules spread over 287 sites. Disorder is modelled over two conformations for 30 amino-acid side chains. The final weighted R index on F(2) (wR(2)) on all data was 30.4%. Conventional R indices based on F were 14.2 and 11.8% for all data and for data with F > 4sigma(F), respectively.

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Organizational Affiliation: 
• Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, CA 94550, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.72 kDa 
• Atom Count: 2,163 
• 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
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.167 (Depositor) 
• R-Value Work:  0.175 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.954	α = 90
b = 86.053	β = 90
c = 89.079	γ = 90

Software Package:

Software Name	Purpose
SHELXL-92	model building
SHELXL-92	refinement
ADSC	data collection
SHELXL-92	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Parkin, S., Rupp, B., Hope, H.

Revision History  

• Version 1.0: 1997-02-12
  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: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection