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PDBsum entry 2vb1

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protein ligands links
Hydrolase PDB id
2vb1
Jmol PyMol
Contents
Protein chain
129 a.a. *
Ligands
ACT
EDO ×3
NO3 ×9
Waters ×170
* Residue conservation analysis
PDB id:
2vb1
Name: Hydrolase
Title: Hewl at 0.65 angstrom resolution
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: Gallus gallus. Chicken. Organism_taxid: 9031. Cell: egg
Resolution:
0.65Å     R-factor:   0.083     R-free:   0.095
Authors: J.Wang,M.Dauter,R.Alkire,A.Joachimiak,Z.Dauter
Key ref:
J.Wang et al. (2007). Triclinic lysozyme at 0.65 A resolution. Acta Crystallogr D Biol Crystallogr, 63, 1254-1268. PubMed id: 18084073 DOI: 10.1107/S0907444907054224
Date:
05-Sep-07     Release date:   18-Sep-07    
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   4 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
DOI no: 10.1107/S0907444907054224 Acta Crystallogr D Biol Crystallogr 63:1254-1268 (2007)
PubMed id: 18084073  
 
 
Triclinic lysozyme at 0.65 A resolution.
J.Wang, M.Dauter, R.Alkire, A.Joachimiak, Z.Dauter.
 
  ABSTRACT  
 
The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been refined against diffraction data extending to 0.65 A resolution measured at 100 K using synchrotron radiation. Refinement with anisotropic displacement parameters and with the removal of stereochemical restraints for the well ordered parts of the structure converged with a conventional R factor of 8.39% and an R(free) of 9.52%. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. In addition to the 129-residue protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and three ethylene glycol molecules were located in the electron-density map. Eight sections of the main chain and many side chains were modeled with alternate conformations. The occupancies of the water sites were refined and this step is meaningful when assessed by use of the free R factor. A detailed description and comparison of the structure are made with reference to the previously reported triclinic HEWL structures refined at 0.925 A (at the low temperature of 120 K) and at 0.95 A resolution (at room temperature).
 
  Selected figure(s)  
 
Figure 5.
Figure 5 (a) Distribution of the N-C^ -C angles for the current model and (b) for 3lzt . (c) Modeling the peptide flip around Asn103 in 3lzt and (d) in the current model. Blue and red colours in (a) correspond to residues in single and double conformations, respectively.
Figure 9.
Figure 9 Distributions of peptide-bond lengths for well ordered parts of the model. Red columns represent restrained refinement and green columns unrestrained refinement.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 1254-1268) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20516622 A.Higashiura, T.Kurakane, M.Matsuda, M.Suzuki, K.Inaka, M.Sato, T.Kobayashi, T.Tanaka, H.Tanaka, K.Fujiwara, and A.Nakagawa (2010).
High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 698-708.
PDB code: 3klr
20488725 B.Reiz, and L.Li (2010).
Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.
  J Am Soc Mass Spectrom, 21, 1596-1605.  
19543291 C.A.Velikovsky, L.Deng, S.Tasumi, L.M.Iyer, M.C.Kerzic, L.Aravind, Z.Pancer, and R.A.Mariuzza (2009).
Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.
  Nat Struct Mol Biol, 16, 725-730.
PDB codes: 3g39 3g3a 3g3b
19678839 W.Bialek, S.Krzywda, M.Jaskolski, and A.Szczepaniak (2009).
Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion.
  FEBS J, 276, 4426-4436.
PDB code: 3dr0
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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