spacer
spacer

PDBsum entry 2c8o

Go to PDB code: 
protein links
Hydrolase PDB id
2c8o
Jmol
Contents
Protein chain
129 a.a. *
Waters ×133
* Residue conservation analysis
PDB id:
2c8o
Name: Hydrolase
Title: Lysozyme (1sec) and uv lasr excited fluorescence
Structure: LysozymE C. Chain: a. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d 4, gal d iv. Ec: 3.2.1.17
Source: Synthetic: yes. Gallus gallus. Chicken. Organism_taxid: 9031. Cell_line: white egg. Other_details: sigma-aldrich
Resolution:
1.5Å     R-factor:   0.196     R-free:   0.208
Authors: X.Vernede,B.Lavault,J.Ohana,D.Nurizzo,J.Joly,L.Jacquamet, F.Felisaz,F.Cipriani,D.Bourgeois
Key ref:
X.Vernede et al. (2006). UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops. Acta Crystallogr D Biol Crystallogr, 62, 253-261. PubMed id: 16510972 DOI: 10.1107/S0907444905041429
Date:
06-Dec-05     Release date:   08-Mar-06    
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/S0907444905041429 Acta Crystallogr D Biol Crystallogr 62:253-261 (2006)
PubMed id: 16510972  
 
 
UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops.
X.Vernede, B.Lavault, J.Ohana, D.Nurizzo, J.Joly, L.Jacquamet, F.Felisaz, F.Cipriani, D.Bourgeois.
 
  ABSTRACT  
 
Structural proteomics has promoted the rapid development of automated protein structure determination using X-ray crystallography. Robotics are now routinely used along the pipeline from genes to protein structures. However, a bottleneck still remains. At synchrotron beamlines, the success rate of automated sample alignment along the X-ray beam is limited by difficulties in visualization of protein crystals, especially when they are small and embedded in mother liquor. Despite considerable improvement in optical microscopes, the use of visible light transmitted or reflected by the sample may result in poor or misleading contrast. Here, the endogenous fluorescence from aromatic amino acids has been used to identify even tiny or weakly fluorescent crystals with a high success rate. The use of a compact laser at 266 nm in combination with non-fluorescent sample holders provides an efficient solution to collect high-contrast fluorescence images in a few milliseconds and using standard camera optics. The best image quality was obtained with direct illumination through a viewing system coaxial with the UV beam. Crystallographic data suggest that the employed UV exposures do not generate detectable structural damage.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Fluorescence images recorded with the standard setup. A crystal of cephamycinase 2 ( [127]~ 20 Ám in thickness) is shown in three different orientations in visible light (a) or UV light (b). Red points show the crystal centre as detected by the C3D software. The crystal is hardly detectable in visible light, so that C3D fails to identify it correctly in orientations 2 and 3. In contrast, the crystal is easily identified under UV-laser illumination by both the user and the software, whatever the loop orientation.
Figure 7.
Figure 7 Effect of UV-induced radiation damage. Experimental difference electron-density maps (F[obs-UV] - F[obs-noUV]) are shown for insulin. Maps are contoured at ▒5.0 , where is the standard deviation of the electron-density difference (red, negative; green, positive) and are overlaid on a model of non-irradiated insulin. (a) Overall view of the protein for a 1 s exposure to 266 nm laser light (the same difference map displayed at ▒3.0 is also featureless and shows only noise peaks). (b) The same view of the protein for a 60 s exposure to 266 nm laser light (with identical power density as in a). (c) Example of a damaged disulfide bridge. Breakage of the CysA7-CysB7 bridge is clearly visible, together with a significant displacement of the main-chain carbonyl group of CysA7. The maps were calculated using CCP4 (Collaborative Computational Project, Number 4, 1994[Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.]). This figure was drawn using BOBSCRIPT (Esnouf, 1999[Esnouf, R. M. (1999). Acta Cryst. D55, 938-940.]) and RASTER3D (Merritt & Bacon, 1997[Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 253-261) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525645 D.de Sanctis, P.A.Tucker, and S.Panjikar (2011).
Additional phase information from UV damage of selenomethionine labelled proteins.
  J Synchrotron Radiat, 18, 374-380.  
20693689 D.Watts, J.Müller-Dieckmann, G.Tsakanova, V.S.Lamzin, and M.R.Groves (2010).
Quantitive evaluation of macromolecular crystallization experiments using 1,8-ANS fluorescence.
  Acta Crystallogr D Biol Crystallogr, 66, 901-908.  
  20208182 H.S.Gill (2010).
Evaluating the efficacy of tryptophan fluorescence and absorbance as a selection tool for identifying protein crystals.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 364-372.  
20526815 M.Cymborowski, M.Klimecka, M.Chruszcz, M.D.Zimmerman, I.A.Shumilin, D.Borek, K.Lazarski, A.Joachimiak, Z.Otwinowski, W.Anderson, and W.Minor (2010).
To automate or not to automate: this is the question.
  J Struct Funct Genomics, 11, 211-221.  
18210369 B.A.Manjasetty, A.P.Turnbull, S.Panjikar, K.Büssow, and M.R.Chance (2008).
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.
  Proteomics, 8, 612-625.  
17959373 T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.
  Curr Opin Struct Biol, 17, 580-586.  
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.