2CHR

A RE-EVALUATION OF THE CRYSTAL STRUCTURE OF CHLOROMUCONATE CYCLOISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A re-evaluation of the crystal structure of chloromuconate cycloisomerase.

Kleywegt, G.J.Hoier, H.Jones, T.A.

(1996) Acta Crystallogr.,Sect.D 52: 858-863

  • DOI: 10.1107/S0907444995008936

  • PubMed 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 incorr ...

    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).


    Related Citations: 
    • Crystal Structure of Chloromuconate Cycloisomerase from Alcaligenes Eutrophus Jmp134 (Pjp4) at 3 Angstroms Resolution
      Hoier, H.,Schloemann, M.,Hammer, A.,Glusker, J.P.,Carrell, H.L.,Goldman, A.,Stezowski, J.J.,Heinemann, U.
      (1994) Acta Crystallogr.,Sect.D 50: 75


    Organizational Affiliation

    Department of Molecular Biology, Biomedical Centre, Uppsala University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHLOROMUCONATE CYCLOISOMERASE
A
370Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)Gene Names: tfdDI (tfdD)
EC: 5.5.1.7
Find proteins for P05404 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197))
Go to UniProtKB:  P05404
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.890α = 90.00
b = 111.890β = 90.00
c = 148.490γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance