1LOE

X-RAY CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 1.9 ANGSTROMS RESOLUTION OF ISOLECTIN I FROM THE SEEDS OF LATHYRUS OCHRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.185 

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Literature

X-ray crystal structure determination and refinement at 1.9 A resolution of isolectin I from the seeds of Lathyrus ochrus.

Bourne, Y.Abergel, C.Cambillau, C.Frey, M.Rouge, P.Fontecilla-Camps, J.C.

(1990) J.Mol.Biol. 214: 571-584

  • DOI: 10.1016/0022-2836(90)90199-V

  • PubMed Abstract: 
  • Orthorhombic crystals of isolectin I (LOLI) from the seeds of Lathyrus ochrus were first obtained during the STS 29 space shuttle mission. Subsequently, isostructural crystals were also obtained in the laboratory. They belong to the space group P2(1) ...

    Orthorhombic crystals of isolectin I (LOLI) from the seeds of Lathyrus ochrus were first obtained during the STS 29 space shuttle mission. Subsequently, isostructural crystals were also obtained in the laboratory. They belong to the space group P2(1)2(1)2, with cell dimensions a = 135.84 A, b = 63.12 A and c = 54.54 A with one functional entity, a dimer, in the asymmetric unit (Vm = 2.2 A3/Da). The three-dimensional structure of LOLI, which was solved by the molecular replacement method using a 3 A resolution model of pea lectin, has subsequently been refined by using crystallographic data between 8.0 A and 1.9 A resolution, coupled to molecular dynamics and energy minimization techniques. The conventional R-factor is 0.185 for Fo greater than 1 sigma(Fo). The final model includes 220 well-defined water molecules and has root-mean-square deviations from ideal bond distances and angles of 0.004 A and 3 degrees, respectively. Only slight conformation differences have been found between the two alpha beta monomers. The molecular structure of LOLI, the first to be determined from the genus Lathyrus, is very similar to those of concanavalin A, pea lectin and favin. Differences are confined to the loop regions and beta-chain termini. Comparison of equivalent C alpha atom positions between our final model and the pea lectin structure shows slight differences in the association of the two monomers, which are probably due to the different environments in the crystals. The root-mean-square deviation between C alpha atoms of LOLI and pea lectin is 0.40 A. The metal binding sites are very similar in pea lectin, concanavalin A and LOLI. The sugar-binding sites of LOLI are occupied by four well-ordered water molecules each. The cleavage site for one of the monomers is specially well defined in the final electron density map: the amino group of Glul (alpha) seems to form a salt bridge with the carboxylate group of the terminal Asn181 (beta). A detailed analysis of the difference in crystal packing contacts between pea lectin and LOLI shows that, as might be expected, several of the intermolecular interactions are mediated by residues that correspond to substitutions in the LOLI amino acid sequence.


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallisation des Macromolécules Biologiques, URA 232-CNRS, Faculté de Médecine Secteur-Nord, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEGUME ISOLECTIN I (ALPHA CHAIN)
A, C
181Lathyrus ochrusN/A
Find proteins for P04122 (Lathyrus ochrus)
Go to UniProtKB:  P04122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEGUME ISOLECTIN I (BETA CHAIN)
B, D
52Lathyrus ochrusN/A
Find proteins for P12306 (Lathyrus ochrus)
Go to UniProtKB:  P12306
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.840α = 90.00
b = 63.120β = 90.00
c = 54.540γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance