PDBsum entry 2g4l

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Lyase PDB id
Jmol PyMol
Protein chain
256 a.a. *
SO4 ×5
Waters ×181
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Anomalous substructure of hydroxynitrile lyase
Structure: (S)-acetone-cyanohydrin lyase. Chain: a. Synonym: s-hydroxynitrile lyase, s-hydroxynitrilase, oxynit ec:
Source: Hevea brasiliensis. Organism_taxid: 3981
1.84Å     R-factor:   0.177     R-free:   0.197
Authors: C.Mueller-Dieckmann,M.S.Weiss
Key ref:
C.Mueller-Dieckmann et al. (2007). On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Acta Crystallogr D Biol Crystallogr, 63, 366-380. PubMed id: 17327674 DOI: 10.1107/S0907444906055624
22-Feb-06     Release date:   20-Feb-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P52704  (HNL_HEVBR) -  (S)-hydroxynitrile lyase
257 a.a.
256 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - (S)-hydroxynitrile lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. An aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone
2. An aromatic (S)-hydroxynitrile = cyanide + an aromatic aldehyde
aliphatic (S)-hydroxynitrile
= cyanide
+ aliphatic aldehyde or ketone
aromatic (S)-hydroxynitrile
= cyanide
+ aromatic aldehyde
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     aliphatic (S)-hydroxynitrile lyase activity     3 terms  


DOI no: 10.1107/S0907444906055624 Acta Crystallogr D Biol Crystallogr 63:366-380 (2007)
PubMed id: 17327674  
On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, M.S.Weiss.
23 different crystal forms of 19 different biological macromolecules were examined with respect to their anomalously scattering substructures using diffraction data collected at a wavelength of 2.0 A (6.2 keV). In more than 90% of the cases the substructure was found to contain more than just the protein S atoms. The data presented suggest that chloride, sulfate, phosphate or metal ions from the buffer or even from the purification protocol are frequently bound to the protein molecule and that these ions are often overlooked, especially if they are not bound at full occupancy. Thus, in order to fully describe the macromolecule under study, it seems desirable that any structure determination be complemented with a long-wavelength data set.
  Selected figure(s)  
Figure 1.
Figure 1 Anomalous scattering length ( f''] ) values in units of electrons at = 1.0 Å (red) and = 2.0 Å (green) for elements 11-20 according to Cromer & Liberman (1970[Cromer, D. & Liberman, D. (1970). J. Chem. Phys. 53, 1891-1898.]).
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 366-380) copyright 2007.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
21460452 R.J.Read, and A.J.McCoy (2011).
Using SAD data in Phaser.
  Acta Crystallogr D Biol Crystallogr, 67, 338-344.  
21525646 R.M.Leal, G.P.Bourenkov, O.Svensson, D.Spruce, M.Guijarro, and A.N.Popov (2011).
Experimental procedure for the characterization of radiation damage in macromolecular crystals.
  J Synchrotron Radiat, 18, 381-386.  
20382985 G.L.Taylor (2010).
Introduction to phasing.
  Acta Crystallogr D Biol Crystallogr, 66, 325-338.  
20724792 J.Gabadinho, A.Beteva, M.Guijarro, V.Rey-Bakaikoa, D.Spruce, M.W.Bowler, S.Brockhauser, D.Flot, E.J.Gordon, D.R.Hall, B.Lavault, A.A.McCarthy, J.McCarthy, E.Mitchell, S.Monaco, C.Mueller-Dieckmann, D.Nurizzo, R.B.Ravelli, X.Thibault, M.A.Walsh, G.A.Leonard, and S.M.McSweeney (2010).
MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments.
  J Synchrotron Radiat, 17, 700-707.  
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
19219048 A.Guskov, J.Kern, A.Gabdulkhakov, M.Broser, A.Zouni, and W.Saenger (2009).
Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride.
  Nat Struct Mol Biol, 16, 334-342.
PDB codes: 3bz1 3bz2
19581484 B.Z.Wang, P.Guo, B.J.Hang, L.Li, J.He, and S.P.Li (2009).
Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product.
  Appl Environ Microbiol, 75, 5496-5500.  
  19255463 S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, and A.McPherson (2009).
High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 192-198.
PDB code: 3dyb
  18323597 C.Mueller-Dieckmann, S.Kernstock, J.Mueller-Dieckmann, M.S.Weiss, and F.Koch-Nolte (2008).
Structure of mouse ADP-ribosylhydrolase 3 (mARH3).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 156-162.
PDB code: 2qty
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