spacer
spacer

PDBsum entry 2jic

Go to PDB code: 
protein links
Hydrolase PDB id
2jic
Jmol
Contents
Protein chain
189 a.a. *
Waters ×138
* Residue conservation analysis
PDB id:
2jic
Name: Hydrolase
Title: High resolution structure of xylanase-ii from one micron beam experiment
Structure: Xylanase-ii. Chain: a. Ec: 3.2.1.8
Source: Trichoderma longibrachiatum. Organism_taxid: 5548
Resolution:
1.50Å     R-factor:   0.181     R-free:   0.203
Authors: R.Moukhametzianov,M.Burghammer,P.C.Edwards,S.Petitdemange, D.Popov,M.Fransen,G.F.Schertler,C.Riekel
Key ref:
R.Moukhametzianov et al. (2008). Protein crystallography with a micrometre-sized synchrotron-radiation beam. Acta Crystallogr D Biol Crystallogr, 64, 158-166. PubMed id: 18219115 DOI: 10.1107/S090744490705812X
Date:
27-Feb-07     Release date:   13-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
F8W669  (F8W669_TRILO) -  Endo-1,4-beta-xylanase
Seq:
Struc:
190 a.a.
189 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.8  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1107/S090744490705812X Acta Crystallogr D Biol Crystallogr 64:158-166 (2008)
PubMed id: 18219115  
 
 
Protein crystallography with a micrometre-sized synchrotron-radiation beam.
R.Moukhametzianov, M.Burghammer, P.C.Edwards, S.Petitdemange, D.Popov, M.Fransen, G.McMullan, G.F.Schertler, C.Riekel.
 
  ABSTRACT  
 
For the first time, protein microcrystallography has been performed with a focused synchrotron-radiation beam of 1 microm using a goniometer with a sub-micrometre sphere of confusion. The crystal structure of xylanase II has been determined with a flux density of about 3 x 10(10) photons s(-1) microm(-2) at the sample. Two sets of diffraction images collected from different sized crystals were shown to comprise data of good quality, which allowed a 1.5 A resolution xylanase II structure to be obtained. The main conclusion of this experiment is that a high-resolution diffraction pattern can be obtained from 20 microm(3) crystal volume, corresponding to about 2 x 10(8) unit cells. Despite the high irradiation dose in this case, it was possible to obtain an excellent high-resolution map and it could be concluded from the individual atomic B-factor patterns that there was no evidence of significant radiation damage. The photoelectron escape from a narrow diffraction channel is a possible reason for reduced radiation damage as indicated by Monte Carlo simulations. These results open many new opportunities in scanning protein microcrystallography and make random data collection from microcrystals a real possibility, therefore enabling structures to be solved from much smaller crystals than previously anticipated as long as the crystallites are well ordered.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Schematic design and distance indications of the undulator source and optics. A, low- undulator source; B, primary slits; C, double Si(111) monochromator; D, secondary slits in front of a Kirkpatrick-Baez (KB) mirror; E[1] and E[2], KB mirrors; F: micromanipulator and goniometer. The size and divergence of the beam at the undulator source point and at the focal spot are symbolized by squares. The distance from the source and the beam divergence are indicated.
Figure 4.
Figure 4 Diffraction pattern of xylanase II. (a), (b), (c): Spot shapes for reflections of high, medium and low resolution, respectively, with different magnitude of counts. (d), (e), (f): Normalized standard profiles (background pixels, 0; peak pixels are shown as a histogram within the range {1-9, A-Z}) accumulated in MOSFLM from spots of several adjacent images within a certain detector area. The detector pixel size is 78.94 × 78.94 µm. The shape of low- and medium-resolution spots is mainly defined by the detector point-spread function. Average profiles do not adequately fit the individual spot shape for strong spots at low resolution, therefore in this resolution range integration by summation of pixels is superior to profile fitting. A weighted integration scheme described in the text was used to find the best compromise.
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 158-166) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23407534 A.J.Venkatakrishnan, X.Deupi, G.Lebon, C.G.Tate, G.F.Schertler, and M.M.Babu (2013).
Molecular signatures of G-protein-coupled receptors.
  Nature, 494, 185-194.  
21478852 R.M.Bill, P.J.Henderson, S.Iwata, E.R.Kunji, H.Michel, R.Neutze, S.Newstead, B.Poolman, C.G.Tate, and H.Vogel (2011).
Overcoming barriers to membrane protein structure determination.
  Nat Biotechnol, 29, 335-340.  
21444772 R.Sanishvili, D.W.Yoder, S.B.Pothineni, G.Rosenbaum, S.Xu, S.Vogt, S.Stepanov, O.A.Makarov, S.Corcoran, R.Benn, V.Nagarajan, J.L.Smith, and R.F.Fischetti (2011).
Radiation damage in protein crystals is reduced with a micron-sized X-ray beam.
  Proc Natl Acad Sci U S A, 108, 6127-6132.  
20662638 C.Nicolini, and E.Pechkova (2010).
Nanoproteomics for nanomedicine.
  Nanomedicine (Lond), 5, 677-682.  
20975219 C.Riekel, M.Burghammer, R.J.Davies, E.Di Cola, C.König, H.T.Lemke, J.L.Putaux, and S.Schöder (2010).
Raster microdiffraction with synchrotron radiation of hydrated biopolymers with nanometre step-resolution: case study of starch granules.
  J Synchrotron Radiat, 17, 743-750.  
20029119 D.Flot, T.Mairs, T.Giraud, M.Guijarro, M.Lesourd, V.Rey, D.van Brussel, C.Morawe, C.Borel, O.Hignette, J.Chavanne, D.Nurizzo, S.McSweeney, and E.Mitchell (2010).
The ID23-2 structural biology microfocus beamline at the ESRF.
  J Synchrotron Radiat, 17, 107-118.  
20382986 E.F.Garman (2010).
Radiation damage in macromolecular crystallography: what is it and why should we care?
  Acta Crystallogr D Biol Crystallogr, 66, 339-351.  
20382994 G.P.Bourenkov, and A.N.Popov (2010).
Optimization of data collection taking radiation damage into account.
  Acta Crystallogr D Biol Crystallogr, 66, 409-419.  
  20823545 J.Hausmann, E.Christodoulou, M.Kasiem, V.De Marco, L.A.van Meeteren, W.H.Moolenaar, D.Axford, R.L.Owen, G.Evans, and A.Perrakis (2010).
Mammalian cell expression, purification, crystallization and microcrystal data collection of autotaxin/ENPP2, a secreted mammalian glycoprotein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1130-1135.  
20382993 J.M.Holton, and K.A.Frankel (2010).
The minimum crystal size needed for a complete diffraction data set.
  Acta Crystallogr D Biol Crystallogr, 66, 393-408.  
20693684 M.W.Bowler, M.Guijarro, S.Petitdemange, I.Baker, O.Svensson, M.Burghammer, C.Mueller-Dieckmann, E.J.Gordon, D.Flot, S.M.McSweeney, and G.A.Leonard (2010).
Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.
  Acta Crystallogr D Biol Crystallogr, 66, 855-864.  
20460858 M.Yamamoto, K.Hirata, T.Hikima, Y.Kawano, and G.Ueno (2010).
[Protein micro-crystallography with a new micro-beam beamline].
  Yakugaku Zasshi, 130, 641-648.  
20157276 R.E.Gillilan, M.J.Cook, S.W.Cornaby, and D.H.Bilderback (2010).
Microcrystallography using single-bounce monocapillary optics.
  J Synchrotron Radiat, 17, 227-236.  
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
20057043 S.Cornaby, D.M.Szebenyi, D.M.Smilgies, D.J.Schuller, R.Gillilan, Q.Hao, and D.H.Bilderback (2010).
Feasibility of one-shot-per-crystal structure determination using Laue diffraction.
  Acta Crystallogr D Biol Crystallogr, 66, 2.  
20538452 V.P.Jaakola, and A.P.Ijzerman (2010).
The crystallographic structure of the human adenosine A2A receptor in a high-affinity antagonist-bound state: implications for GPCR drug screening and design.
  Curr Opin Struct Biol, 20, 401-414.  
19339946 D.T.Lodowski, and K.Palczewski (2009).
Chemokine receptors and other G protein-coupled receptors.
  Curr Opin HIV AIDS, 4, 88-95.  
19240333 R.F.Fischetti, S.Xu, D.W.Yoder, M.Becker, V.Nagarajan, R.Sanishvili, M.C.Hilgart, S.Stepanov, O.Makarov, and J.L.Smith (2009).
Mini-beam collimator enables microcrystallography experiments on standard beamlines.
  J Synchrotron Radiat, 16, 217-225.  
19535414 V.Cherezov, M.A.Hanson, M.T.Griffith, M.C.Hilgart, R.Sanishvili, V.Nagarajan, S.Stepanov, R.F.Fischetti, P.Kuhn, and R.C.Stevens (2009).
Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 microm size X-ray synchrotron beam.
  J R Soc Interface, 6, S587-S597.  
19436492 T.R.Schneider (2008).
Synchrotron radiation: micrometer-sized x-ray beams as fine tools for macromolecular crystallography.
  HFSP J, 2, 302-306.  
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.