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PDBsum entry 1d3f
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protein ligands metals links
Hydrolase PDB id
1d3f

 

 

 

 

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Contents
Protein chain
162 a.a. *
Ligands
HED
Metals
_CL ×2
Waters ×116
* Residue conservation analysis
PDB id:
1d3f
Name: Hydrolase
Title: N-terminal domain core methionine mutation
Structure: Lysozyme. Chain: a. Engineered: yes. Mutation: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665. Gene: gene e. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.05Å     R-factor:   0.159    
Authors: N.C.Gassner,B.W.Matthews
Key ref: N.C.Gassner and B.W.Matthews (1999). Use of differentially substituted selenomethionine proteins in X-ray structure determination. Acta Crystallogr D Biol Crystallogr, 55, 1967-1970. PubMed id: 10666571
Date:
29-Sep-99     Release date:   08-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4
Seq:
Struc: 		164 a.a.
162 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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.

 

 
Acta Crystallogr D Biol Crystallogr 55:1967-1970 (1999)
PubMed id: 10666571  
 
 
Use of differentially substituted selenomethionine proteins in X-ray structure determination.
N.C.Gassner, B.W.Matthews.
 
  ABSTRACT  
 
Using heavily methionine-substituted T4 lysozyme as an example, it is shown how the addition or deletion of a small number of methionines can simplify the location of selenium sites for use in MAD phasing. By comparing the X-ray data for a large number of singly substituted lysozymes, it is shown that the optimal amino acid to be substituted by methionine is leucine, followed, in order of preference, by phenylalanine, isoleucine and valine. The identification of leucine as the first choice agrees with the ranking suggested by the Dayhoff mutation probability, i.e. by the frequency of amino-acid substitutions in the sequences of related proteins. The ranking of the second and subsequent choices, however, differ significantly.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159471 C.L.Keiski, M.Harwich, S.Jain, A.M.Neculai, P.Yip, H.Robinson, J.C.Whitney, L.Riley, L.L.Burrows, D.E.Ohman, and P.L.Howell (2010).
AlgK is a TPR-containing protein and the periplasmic component of a novel exopolysaccharide secretin.
  Structure, 18, 265-273.
PDB code: 3e4b
20818390 D.Sun, G.Lee, J.H.Lee, H.Y.Kim, H.W.Rhee, S.Y.Park, K.J.Kim, Y.Kim, B.Y.Kim, J.I.Hong, C.Park, H.E.Choy, J.H.Kim, Y.H.Jeon, and J.Chung (2010).
A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses.
  Nat Struct Mol Biol, 17, 1188-1194.
PDB codes: 3nqw 3nr1
  19255477 H.Koskiniemi, T.Grocholski, G.Schneider, and J.Niemi (2009).
Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 256-259.  
16501089 H.Ding, T.J.Green, S.Lu, and M.Luo (2006).
Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus.
  J Virol, 80, 2808-2814.
PDB code: 2fqm
16926157 N.Brot, J.F.Collet, L.C.Johnson, T.J.Jönsson, H.Weissbach, and W.T.Lowther (2006).
The thioredoxin domain of Neisseria gonorrhoeae PilB can use electrons from DsbD to reduce downstream methionine sulfoxide reductases.
  J Biol Chem, 281, 32668-32675.
PDB code: 2h30
  16511173 B.Gao, A.Bertrand, W.H.Boles, H.R.Ellis, and T.C.Mallett (2005).
Crystallization and preliminary X-ray crystallographic studies of the alkanesulfonate FMN reductase from Escherichia coli.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 837-840.  
16338414 H.Fan, A.Ooi, Y.W.Tan, S.Wang, S.Fang, D.X.Liu, and J.Lescar (2005).
The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties.
  Structure, 13, 1859-1868.
PDB codes: 2btl 2bxx
15130476 M.Graille, S.Quevillon-Cheruel, N.Leulliot, C.Z.Zhou, I.Li de la Sierra Gallay, L.Jacquamet, J.L.Ferrer, D.Liger, A.Poupon, J.Janin, and H.van Tilbeurgh (2004).
Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family.
  Structure, 12, 839-847.
PDB codes: 1qvv 1qvw 1qvz
11006535 S.E.Ealick (2000).
Advances in multiple wavelength anomalous diffraction crystallography.
  Curr Opin Chem Biol, 4, 495-499.  
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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