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PDBsum entry 1c57
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protein metals links
Sugar binding protein PDB id
1c57

 

 

 

 

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Contents
Protein chain
237 a.a. *
Metals
_CA
_MN
Waters ×444
* Residue conservation analysis
PDB id:
1c57
Name: Sugar binding protein
Title: Direct determination of the positions of deuterium atoms of bound water in concanavalin a by neutron laue crystallography
Structure: Concanavalin-br. Chain: a. Synonym: concanavalin a, con br
Source: Canavalia ensiformis. Jack bean. Organism_taxid: 3823
Biol. unit: Tetramer (from PDB file)
Authors: J.Habash,J.Raftery,R.Nuttall,H.J.Price,M.S.Lehmann,C.Wilkinson, A.J.Kalb,J.R.Helliwell
Key ref:
J.Habash et al. (2000). Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography. Acta Crystallogr D Biol Crystallogr, 56, 541-550. PubMed id: 10771422 DOI: 10.1107/S0907444900002353
Date:
26-Oct-99     Release date:   08-May-00    
PROCHECK
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 Headers
 References

Protein chain
P55915  (CONA_CANBR) -  Concanavalin-Br from Canavalia brasiliensis
Seq:
Struc: 		237 a.a.
237 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
DOI no: 10.1107/S0907444900002353 Acta Crystallogr D Biol Crystallogr 56:541-550 (2000)
PubMed id: 10771422  
 
 
Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography.
J.Habash, J.Raftery, R.Nuttall, H.J.Price, C.Wilkinson, A.J.Kalb, J.R.Helliwell.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 A water molecule (number 6 in the PDB file) in stereo showing the orientation of D[2]O in the nuclear density (at 1.5 ). 		Figure 2.
Figure 2 The 2F[o] - F[c] neutron-density map (at 1.5 r.m.s.) in stereo around the Mn coordination sphere of ligands.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 541-550) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19255494 W.R.Novak, A.G.Moulin, M.P.Blakeley, I.Schlichting, G.A.Petsko, and D.Ringe (2009).
A preliminary neutron diffraction study of gamma-chymotrypsin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 317-320.  
16897039 F.Meilleur, D.A.Myles, and M.P.Blakeley (2006).
Neutron Laue macromolecular crystallography.
  Eur Biophys J, 35, 611-620.  
16673077 F.Meilleur, E.H.Snell, M.J.van der Woerd, R.A.Judge, and D.A.Myles (2006).
A quasi-Laue neutron crystallographic study of D-xylose isomerase.
  Eur Biophys J, 35, 601-609.  
  16511248 M.Budayova-Spano, S.Z.Fisher, M.T.Dauvergne, M.Agbandje-McKenna, D.N.Silverman, D.A.Myles, and R.McKenna (2006).
Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 6-9.
PDB code: 2ax2
16640829 M.Garg, A.Asthana, H.B.Agashe, G.P.Agrawal, and N.K.Jain (2006).
Stavudine-loaded mannosylated liposomes: in-vitro anti-HIV-I activity, tissue distribution and pharmacokinetics.
  J Pharm Pharmacol, 58, 605-616.  
16622654 M.P.Blakeley, A.Mitschler, I.Hazemann, F.Meilleur, D.A.Myles, and A.Podjarny (2006).
Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex.
  Eur Biophys J, 35, 577-583.  
15546977 B.L.Hanson (2004).
Getting protein solvent structures down cold.
  Proc Natl Acad Sci U S A, 101, 16393-16394.
PDB code: 1xqn
15272083 K.Kurihara, I.Tanaka, T.Chatake, M.W.Adams, F.E.Jenney, N.Moiseeva, R.Bau, and N.Niimura (2004).
Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules.
  Proc Natl Acad Sci U S A, 101, 11215-11220.
PDB code: 1vcx
15525703 M.P.Blakeley, A.J.Kalb, J.R.Helliwell, and D.A.Myles (2004).
The 15-K neutron structure of saccharide-free concanavalin A.
  Proc Natl Acad Sci U S A, 101, 16405-16410.  
12937341 N.Engler, A.Ostermann, N.Niimura, and F.G.Parak (2003).
Hydrogen atoms in proteins: positions and dynamics.
  Proc Natl Acad Sci U S A, 100, 10243-10248.  
12557193 T.Chatake, A.Ostermann, K.Kurihara, F.G.Parak, and N.Niimura (2003).
Hydration in proteins observed by high-resolution neutron crystallography.
  Proteins, 50, 516-523.  
12202382 C.Bon, A.J.Dianoux, M.Ferrand, and M.S.Lehmann (2002).
A model for water motion in crystals of lysozyme based on an incoherent quasielastic neutron-scattering study.
  Biophys J, 83, 1578-1588.  
11709171 P.Martin, S.DeMel, J.Shi, T.Gladysheva, D.L.Gatti, B.P.Rosen, and B.F.Edwards (2001).
Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme.
  Structure, 9, 1071-1081.
PDB codes: 1i9d 1j9b 1jzw
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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