1C57

DIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND WATER IN CONCANAVALIN A BY NEUTRON LAUE CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 

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This is version 1.5 of the entry. See complete history


Literature

Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography.

Habash, J.Raftery, J.Nuttall, R.Price, H.J.Wilkinson, C.Kalb, A.J.Helliwell, J.R.

(2000) Acta Crystallogr D Biol Crystallogr 56: 541-550

  • DOI: https://doi.org/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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Concanavalin-Br237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P55915 (Canavalia brasiliensis)
Explore P55915 
Go to UniProtKB:  P55915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55915
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 
  • 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
INTLAUEdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-08
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Database references, Structure summary
  • Version 1.4: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations