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PDBsum entry 1hf4
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1hf4

 

 

 

 

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Contents
Protein chains
129 a.a. *
Ligands
NO3 ×8
Metals
_NA ×2
Waters ×251
* Residue conservation analysis
PDB id:
1hf4
Name: Hydrolase
Title: Structural effects of monovalent anions on polymorphic lysozyme crystals
Structure: Lysozyme. Chain: a, b. Synonym: hen (gallus gallus) egg-white lysozyme, mucopeptide, n- acetylmuramyl hydrolase. Ec: 3.2.1.17
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: egg white. Cellular_location: cytoplasm (white)
Resolution:
1.45Å     R-factor:   0.215     R-free:   0.256
Authors: M.C.Vaney,I.Broutin,M.Ries-Kautt,A.Ducruix
Key ref:
M.C.Vaney et al. (2001). Structural effects of monovalent anions on polymorphic lysozyme crystals. Acta Crystallogr D Biol Crystallogr, 57, 929-940. PubMed id: 11418760 DOI: 10.1107/S0907444901004504
Date:
29-Nov-00     Release date:   07-Jan-01    
PROCHECK
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 Headers
 References

Protein chains
P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus
Seq:
Struc: 		147 a.a.
129 a.a.
Key:    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.

 

 
DOI no: 10.1107/S0907444901004504 Acta Crystallogr D Biol Crystallogr 57:929-940 (2001)
PubMed id: 11418760  
 
 
Structural effects of monovalent anions on polymorphic lysozyme crystals.
M.C.Vaney, I.Broutin, P.Retailleau, A.Douangamath, S.Lafont, C.Hamiaux, T.Prangé, A.Ducruix, M.Riès-Kautt.
 
  ABSTRACT  
 
Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg-white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85 A, of NaI to 1.6 A, of NaNO(3) to 1.45 A and of KSCN to 1.63 A. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 R.m.s. deviations versus the sequence number between the two independent molecules of the HEWL/NaI monoclinic structure showing the non-equivalence of loops 65-75. 		Figure 6.
Figure 6 All anionic sites (red numbers) aligned on the lysozyme sequence. The unique sites are labelled according to the chemical formula of the anion taken from the corresponding PDB file.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 929-940) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287624 V.Babin, C.Roland, and C.Sagui (2011).
The α-sheet: A missing-in-action secondary structure?
  Proteins, 79, 937-946.  
21432935 Y.R.Gokarn, R.M.Fesinmeyer, A.Saluja, V.Razinkov, S.F.Chase, T.M.Laue, and D.N.Brems (2011).
Effective charge measurements reveal selective and preferential accumulation of anions, but not cations, at the protein surface in dilute salt solutions.
  Protein Sci, 20, 580-587.  
20823548 E.Pozharski (2010).
Percentile-based spread: a more accurate way to compare crystallographic models.
  Acta Crystallogr D Biol Crystallogr, 66, 970-978.  
19706429 Y.Zhang, and P.S.Cremer (2009).
The inverse and direct Hofmeister series for lysozyme.
  Proc Natl Acad Sci U S A, 106, 15249-15253.  
17641629 M.Benvenuti, and S.Mangani (2007).
Crystallization of soluble proteins in vapor diffusion for x-ray crystallography.
  Nat Protoc, 2, 1633-1651.  
12684536 P.E.Mason, G.W.Neilson, C.E.Dempsey, A.C.Barnes, and J.M.Cruickshank (2003).
The hydration structure of guanidinium and thiocyanate ions: implications for protein stability in aqueous solution.
  Proc Natl Acad Sci U S A, 100, 4557-4561.  
12962625 S.Majeed, G.Ofek, A.Belachew, C.C.Huang, T.Zhou, and P.D.Kwong (2003).
Enhancing protein crystallization through precipitant synergy.
  Structure, 11, 1061-1070.
PDB code: 1ps5
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.

 

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