PDBsum entry 2d97

Go to PDB code: 
protein links
Hydrolase PDB id
Protein chain
189 a.a. *
Waters ×111
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of vil-xylanase
Structure: Endo-1,4-beta-xylanase 2. Chain: a. Synonym: xylanase 2, 1,4- beta-d-xylan xylanohydrolase 2. Ec:
Source: Hypocrea jecorina. Organism_taxid: 51453
2.01Å     R-factor:   0.198     R-free:   0.228
Authors: H.Miyatake,T.Hasegawa,A.Yamano
Key ref:
H.Miyatake et al. (2006). New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL). Acta Crystallogr D Biol Crystallogr, 62, 280-289. PubMed id: 16510975 DOI: 10.1107/S0907444905041909
09-Dec-05     Release date:   11-Jul-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P36217  (XYN2_HYPJE) -  Endo-1,4-beta-xylanase 2
222 a.a.
189 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 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   4 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1107/S0907444905041909 Acta Crystallogr D Biol Crystallogr 62:280-289 (2006)
PubMed id: 16510975  
New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL).
H.Miyatake, T.Hasegawa, A.Yamano.
New techniques are presented for the preparation of iodine derivatives, involving vapour diffusion of iodine. Firstly, in the vaporizing iodine labelling (VIL) technique, a small amount of KI/I(2) solution is enclosed in a crystallization well, with the result that gaseous I(2) molecules diffuse into the crystallization droplets without exerting substantial changes in ionic strength in the target crystals. Once they have diffused into the droplet, the I(2) molecules sometimes iodinate accessible tyrosines at ortho positions. Secondly, when iodination is insufficient, the hydrogen peroxide VIL (HYPER-VIL) technique can be further applied to increase the iodination ratio by the addition of a small droplet of hydrogen peroxide (H(2)O(2)) to the crystallization well; the gaseous H(2)O(2) also diffuses into the crystallization droplet to emphasize the iodination. These techniques are most effective for phase determination when coupled with softer X-rays, such as those from Cu Kalpha or Cr Kalpha radiation. The effectiveness of these techniques was assessed using five different crystals. Four of the crystals were successfully iodinated, providing sufficient phasing power for structure determination.
  Selected figure(s)  
Figure 3.
Figure 3 Schematic drawings of iodinated proteins prepared by VIL and HYPER-VIL (depicted using the program NOC; ; the close-up picture of Tyr95 with the electron-density maps in VIL-thaumatin was drawn using the program XtalView). In the molecular pictures, iodinated tyrosines are coloured red, I atoms are in purple and tyrosines that are not involved in iodination are drawn in cyan. (a) Left, VIL-thaumatin with a close-up picture showing around iodinated tyrosine Tyr95 superposed in the I-SAD phased electron-density maps (red > 5 , blue > 1 ); right, HYPER-VIL-thaumatin. (b) HYPER-VIL-trypsin. (c) HYPER-VIL-lysozyme prepared by the HYPER-VIL technique. Iodide I2 is on a special position. (d) Left, VIL-xylanase; right, VIL'-xylanase.
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 280-289) copyright 2006.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18753631 D.N.Ho, N.C.Pomroy, J.A.Cuesta-Seijo, and G.G.Privé (2008).
Crystal structure of a self-assembling lipopeptide detergent at 1.20 A.
  Proc Natl Acad Sci U S A, 105, 12861-12866.
PDB code: 3cay
  18391420 S.J.Wood, X.L.Li, M.A.Cotta, P.Biely, N.E.Duke, M.Schiffer, and P.R.Pokkuluri (2008).
Crystallization and preliminary X-ray diffraction analysis of the glucuronoyl esterase catalytic domain from Hypocrea jecorina.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 255-257.  
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.