1NXD

Crystal structure of MnMn Concanavalin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of concanavalin A at pH 8: bound solvent and crystal contacts.

Lopez-Jaramillo, F.J.Gonzalez-Ramirez, L.A.Albert, A.Santoyo-Gonzalez, F.Vargas-Berenguel, A.Otalora, F.

(2004) Acta Crystallogr.,Sect.D 60: 1048-1056

  • DOI: 10.1107/S0907444904007000

  • PubMed Abstract: 
  • Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The s ...

    Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The structure was solved at 1.9 angstroms, with free R and R values of 0.201 and 0.184, respectively. As expected, no molecules of the ligand were bound to the protein. Soaking in the cryobuffer left its fingerprint as 25 molecules of glycerol in the bound solvent, most of them at specific positions. The fact that a glycerol molecule is located in the sugar-binding pocket of each of the four subunits in the asymmetric unit and another is located in two of the peptide-binding sites suggests a recognition phenomenon rather than a displacement of water molecules by glycerol. Crystal contact analysis shows that a relation exists between the residues that form hydrogen bonds to other asymmetric units and the space group: contact Asp58-Ser62 is a universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and Tyr100-His205 contacts are general features of the C222(1) crystal form.


    Related Citations: 
    • Crystallization and cryocrystallography inside X-ray capillaries
      Lopez-Jaramillo, F.J.,Garcia-Ruiz, J.M.,Gavira, J.A.,Otalora, F.
      (2001) J.Appl.Crystallogr. 34: 365


    Organizational Affiliation

    Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-UGRA, Facultad de Ciencias, Campus Fuentenueva, E-18002 Granada, Spain. javier@lec.ugr.es




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
concanavalin A
1, 2, 3, 4
237Canavalia ensiformisN/A
Find proteins for P02866 (Canavalia ensiformis)
Go to UniProtKB:  P02866
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
1, 2, 3, 4
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
1, 2, 3, 4
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
1, 2, 3, 4
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
1, 2, 3, 4
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.300α = 90.00
b = 118.000β = 90.00
c = 249.500γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
CNSrefinement
MAR345data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-07-05
    Type: Source and taxonomy
  • Version 1.5: 2017-10-11
    Type: Refinement description