1QNY

X-ray refinement of D2O soaked crystal of concanavalin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

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This is version 1.2 of the entry. See complete history


Literature

Direct Determination of the Positions of Deuterium Atoms of Bound Water in Concanavalin a by Neutron Laue Crystallography

Habash, J.Raftery, J.Nuttall, R.Price, H.J.Lehmann, M.S.Wilkinson, C.Kalb(Gilboa), A.J.Helliwell, J.R.

(2000) Acta Crystallogr D Biol Crystallogr 56: 541

  • DOI: 10.1107/s0907444900002353
  • Primary Citation of Related Structures:  
    1C57, 1QNY

  • PubMed Abstract: 
  • The correct positions of the deuterium (D) atoms of many of the bound waters in the protein concanavalin A are revealed by neutron Laue diffraction. The approach includes cases where these water D atoms show enough mobility to render them invisible even to ultra-high resolution synchrotron-radiation X-ray crystallography ...

    The correct positions of the deuterium (D) atoms of many of the bound waters in the protein concanavalin A are revealed by neutron Laue diffraction. The approach includes cases where these water D atoms show enough mobility to render them invisible even to ultra-high resolution synchrotron-radiation X-ray crystallography. The positions of the bound water H atoms calculated on the basis of chemical and energetic considerations are often incorrect. The D-atom positions for the water molecules in the Mn-, Ca- and sugar-binding sites of concanavalin A are described in detail.


    Related Citations: 
    • Neutron Laue Diffraction Study of Concanavalin A:The Proton of Asp28
      Habash, J., Raftery, J., Weisgerber, S., Cassetta, A., Lehmann, M.S., Hoghoj, P., Wilkinson, C., Campbell, J.W., Helliwell, J.R.
      (1997) J Chem Soc Faraday Trans 93: 4313
    • The Structure of Concanavalin a and its Bound Solvent Determined with Small-Molecule Accuracy at 0.94A Resolution
      Deacon, A., Gleichmann, T., Kalb(Gilboa), A.J., Price, H., Raftery, J., Bradbrook, G., Yariv, J., Helliwell, J.R.
      (1997) J Chem Soc Faraday Trans 93: 4305

    Organizational Affiliation

    Section of Structural Chemistry, Department of Chemistry, University of Manchester, Manchester M13 9PL, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CONCANAVALIN AA237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.11α = 90
b = 87.58β = 90
c = 63.26γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance