PDBsum entry 1oad

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Isomerase PDB id
Protein chains
387 a.a. *
MRD ×2
MQD ×2
_MN ×2
_MG ×2
Waters ×911
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Glucose isomerase from streptomyces rubiginosus in p21212 crystal form
Structure: Xylose isomerase. Chain: a, b. Synonym: glucose isomerase. Ec:
Source: Streptomyces rubiginosus. Organism_taxid: 1929
Biol. unit: Tetramer (from PDB file)
1.5Å     R-factor:   0.163     R-free:   0.186
Authors: U.A.Ramagopal,M.Dauter,Z.Dauter
Key ref:
U.A.Ramagopal et al. (2003). SAD manganese in two crystal forms of glucose isomerase. Acta Crystallogr D Biol Crystallogr, 59, 868-875. PubMed id: 12777803 DOI: 10.1107/S0907444903005663
08-Jan-03     Release date:   30-Jan-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P24300  (XYLA_STRRU) -  Xylose isomerase
388 a.a.
387 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
Bound ligand (Het Group name = MQD)
matches with 72.00% similarity
= D-xylulose
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     isomerase activity     4 terms  


    Key reference    
DOI no: 10.1107/S0907444903005663 Acta Crystallogr D Biol Crystallogr 59:868-875 (2003)
PubMed id: 12777803  
SAD manganese in two crystal forms of glucose isomerase.
U.A.Ramagopal, M.Dauter, Z.Dauter.
Glucose isomerase from Streptomyces rubiginosus was crystallized in two forms: I222, with one molecule of 44 kDa in the asymmetric unit, and P2(1)2(1)2, with two unique molecules. The I222 structure is known, but the P2(1)2(1)2 form has not been solved before. X-ray diffraction data for the P2(1)2(1)2 form were collected at a wavelength of 1.54 A and data for the I222 form were collected at three different wavelengths: 1.34, 1.07 and 0.98 A. The amount of anomalous signal from one Mn and eight S atoms in these data sets varies from 1.24% to as low as 0.56%. The dual-space direct-methods program SHELXD, run against the Bijvoet differences, gave a clear solution of all anomalous scatterers for all data sets. The Mn positions only were used for SAD phasing of all four data sets. The electron-density map after density modification, resulting from the phasing of a single-wavelength data set and based purely on the anomalous deltaf" contribution, was clearly interpretable; an almost complete model of the protein was built by wARP without human intervention in all four cases. As far as is known, this is the first time that an anomalous signal as low as 0.6% has successfully been used to determine the structure of a macromolecule.
  Selected figure(s)  
Figure 4.
Figure 4 Mode of packing in the I222 (GI-2, GI-3 and GI-4) crystal form: (a) a view along the a axis and (b) a view along the diagonal between the b and c axes. These figures and Fig. 5-were prepared with BOBSCRIPT (Esnouf, 1999[Esnouf, R. M. (1999). Acta Cryst. D55, 938-940.]).
Figure 5.
Figure 5 Mode of packing in the P2[1]2[1]2 (GI-1) crystal form: (a) a view along the c axis and (b) a view along the ab diagonal.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 868-875) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16216579 W.Shi, C.Zhan, A.Ignatov, B.A.Manjasetty, N.Marinkovic, M.Sullivan, R.Huang, and M.R.Chance (2005).
Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics.
  Structure, 13, 1473-1486.  
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