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PDBsum entry 1lzn

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protein ligands metals links
Hydrolase PDB id
1lzn
Jmol
Contents
Protein chain
129 a.a. *
Ligands
NO3 ×5
DOD ×115
Metals
_NA
Waters ×128
* Residue conservation analysis
PDB id:
1lzn
Name: Hydrolase
Title: Neutron structure of hen egg-white lysozyme
Structure: Protein (lysozyme). Chain: a. Other_details: nitrate ions present
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Cell: egg. Cellular_location: cytoplasm (white)
Authors: C.I.Bon,M.S.Lehmann,C.Wilkinson
Key ref:
C.Bon et al. (1999). Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme. Acta Crystallogr D Biol Crystallogr, 55, 978-987. PubMed id: 10216294 DOI: 10.1107/S0907444998018514
Date:
23-Mar-99     Release date:   01-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
Seq:
Struc:
147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1107/S0907444998018514 Acta Crystallogr D Biol Crystallogr 55:978-987 (1999)
PubMed id: 10216294  
 
 
Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme.
C.Bon, M.S.Lehmann, C.Wilkinson.
 
  ABSTRACT  
 
Triclinic crystals of lysozyme, hydrogen-deuterium exchanged in deuterated solvent, have been studied using neutron quasi-Laue techniques and a newly developed cylinder image-plate detector. The wavelength range employed was from 2.7 to 3.5 A, which gave 9426 significant reflections [F >/= 2sigma(F)] to a resolution limit of 1. 7 A. The deuteration states of the H atoms in the protein molecule were identified, followed by an extensive analysis of the water structure surrounding the protein. The final R factor was 20.4% (Rfree = 22.1%). In total, the 244 observed water molecules form approximately one layer of water around the protein with far fewer water molecules located further away. Water molecules covering the apolar patches make tangential layers at 4-5 A from the surface or form C-H...O contacts, and several water-molecule sites can be identified in the apolar cavities. Many of the water molecules are apparently orientationally disordered, and only 115 out of the 244 water molecules sit in mean single orientations. Comparison of these results with quasi-elastic neutron scattering observations of the water dynamics leads to a picture of the water molecules forming an extended constantly fluctuating network covering the protein surface.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 A water molecule held in place by C-H O contacts only. 2F[o] - F[c] map, omitting the water molecules and contoured at the level. Atom colour codes as in Fig. 3-.
Figure 5.
Figure 5 A string arrangement. Orange map: 2F[o] - F[c], omitting full water molecules and contoured at 2 level. Green map: F[o] - F[c], contoured at the 2.5 level. Atom colour codes as in Fig. 3-.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 978-987) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20541500 B.C.Bennett, and M.Yeager (2010).
The lighter side of a sweet reaction.
  Structure, 18, 657-659.  
  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.  
17641823 K.Malek (2007).
Solute transport in orthorhombic lysozyme crystals: a molecular simulation study.
  Biotechnol Lett, 29, 1865-1873.  
17130456 B.Bennett, P.Langan, L.Coates, M.Mustyakimov, B.Schoenborn, E.E.Howell, and C.Dealwis (2006).
Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate.
  Proc Natl Acad Sci U S A, 103, 18493-18498.
PDB code: 2inq
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.  
16114036 L.R.Forrest, and B.Honig (2005).
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.
  Proteins, 61, 296-309.  
15306381 G.Zaccai (2004).
The effect of water on protein dynamics.
  Philos Trans R Soc Lond B Biol Sci, 359, 1269.  
15306375 J.C.Smith, F.Merzel, A.N.Bondar, A.Tournier, and S.Fischer (2004).
Structure, dynamics and reactions of protein hydration water.
  Philos Trans R Soc Lond B Biol Sci, 359, 1181.  
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
14710189 M.Tehei, B.Franzetti, D.Madern, M.Ginzburg, B.Z.Ginzburg, M.T.Giudici-Orticoni, M.Bruschi, and G.Zaccai (2004).
Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering.
  EMBO Rep, 5, 66-70.  
15754058 V.A.Higman, J.Boyd, L.J.Smith, and C.Redfield (2004).
Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings.
  J Biomol NMR, 30, 327-346.  
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.  
11959992 F.Merzel, and J.C.Smith (2002).
Is the first hydration shell of lysozyme of higher density than bulk water?
  Proc Natl Acad Sci U S A, 99, 5378-5383.  
12491444 T.Steiner (2002).
The hydrogen bond in the solid state.
  Angew Chem Int Ed Engl, 41, 49-76.  
11290333 M.G.Rudolph, J.A.Speir, A.Brunmark, N.Mattsson, M.R.Jackson, P.A.Peterson, L.Teyton, and I.A.Wilson (2001).
The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity.
  Immunity, 14, 231-242.
PDB codes: 1fzj 1fzk 1fzm 1fzo
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.