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PDBsum entry 2chr

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protein metals links
Isomerase PDB id
2chr
Jmol
Contents
Protein chain
370 a.a. *
Metals
_CL
_MN
Waters ×24
* Residue conservation analysis
PDB id:
2chr
Name: Isomerase
Title: A re-evaluation of the crystal structure of chloromuconate cycloisomerase
Structure: Chloromuconate cycloisomerase. Chain: a. Engineered: yes
Source: Cupriavidus necator. Organism_taxid: 106590
Biol. unit: Octamer (from PQS)
Resolution:
3.00Å     R-factor:   0.189     R-free:   0.264
Authors: G.J.Kleywegt,T.A.Jones
Key ref:
G.J.Kleywegt et al. (1996). A re-evaluation of the crystal structure of chloromuconate cycloisomerase. Acta Crystallogr D Biol Crystallogr, 52, 858-863. PubMed id: 15299651 DOI: 10.1107/S0907444995008936
Date:
24-Feb-95     Release date:   31-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05404  (TFDD1_CUPPJ) -  Chloromuconate cycloisomerase
Seq:
Struc:
370 a.a.
370 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.5.1.7  - Chloromuconate cycloisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Muconate Cycloisomerase
      Reaction: 2-chloro-2,5-dihydro-5-oxofuran-2-acetate = 3-chloro-cis,cis-muconate
2-chloro-2,5-dihydro-5-oxofuran-2-acetate
= 3-chloro-cis,cis-muconate
      Cofactor: Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444995008936 Acta Crystallogr D Biol Crystallogr 52:858-863 (1996)
PubMed id: 15299651  
 
 
A re-evaluation of the crystal structure of chloromuconate cycloisomerase.
G.J.Kleywegt, H.Hoier, T.A.Jones.
 
  ABSTRACT  
 
It is shown here that the reported 3 A crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus [Hoier, Schlömann, Hammer, Glusker, Carrell, Goldman, Stezowski & Heinemann (1994). Acta Cryst. D50, 75-84] was refined in the incorrect space group I4. In addition, a stretch of about 25 residues near the N-terminus is out-of-register with the density in the original structure. From the coordinates and structure factors deposited in the Protein Data Bank (PDB), it was possible to determine the correct space group to be I422. The structure was then re-refined, using the original data reduced to I422, to a crystallographic free R factor of 0.264 at 3 A resolution (conventional R factor 0.189). With conservative refinement and rebuilding methods, the errors in the chain tracing could be identified and remedied. Since the two molecules per asymmetric unit in the original structure are actually related by crystallographic symmetry, the observed differences between them are artefacts. In particular, the differences between, and peculiarities of the metal-binding sites are unreal. This case shows the dangers of crystallographic refinement in cases with unfavourable data-to-parameter ratios, and the importance of reducing the number of parameters in such cases to prevent gross errors (for instance, by using NCS constraints). It also demonstrates how the evaluation and monitoring of model quality during the entire refinement and rebuilding process can be used to detect and remedy serious errors. Finally, it presents a strong case in favour of depositing not only model coordinates, but also experimental data (preferably, both merged and unmerged data).
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. A~o, A~p plot (Korn & Rose, 1994) of the two NCS-related CMCI molecules in the original model in space group 14. The solid curve shows the difference betw
Figure 3.
Fig. 3. Comparison of residues 13-42 in the structure of chloromu- conate cycloisomerase. The structure of this segment is shown for (a) the A molecule in the 14 structure, (b) the B molecule in the 14 structure, and (c) our model MI4 in space group 1422. Note that molecules A and B have different conformations for the loop. This illustrates the danger of self-fulfilling prophecies with respect to the refinement of, and differences between 'independent' NCS molecules, in particular (but not exclusively) at low resolution.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 858-863) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12930985 T.Kajander, L.Lehtiö, M.Schlömann, and A.Goldman (2003).
The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.
  Protein Sci, 12, 1855-1864.
PDB code: 1nu5
  9726873 M.D.Vollmer, H.Hoier, H.J.Hecht, U.Schell, J.Gröning, A.Goldman, and M.Schlömann (1998).
Substrate specificity of and product formation by muconate cycloisomerases: an analysis of wild-type enzymes and engineered variants.
  Appl Environ Microbiol, 64, 3290-3299.  
8805582 G.J.Kleywegt, and A.T.Brünger (1996).
Checking your imagination: applications of the free R value.
  Structure, 4, 897-904.  
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.