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PDBsum entry 2q2l

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
2q2l
Jmol
Contents
Protein chains
152 a.a. *
Metals
IOD ×10
_ZN ×2
Waters ×203
* Residue conservation analysis
PDB id:
2q2l
Name: Oxidoreductase
Title: Crystal structure of superoxide dismutase from p. Atrosanguina
Structure: Superoxide dismutase. Chain: a, b. Synonym: copper-zinc superoxide dismutase. Engineered: yes
Source: Potentilla atrosanguinea. Organism_taxid: 487759. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.37Å     R-factor:   0.167     R-free:   0.234
Authors: Y.Manickam,J.Gill,P.C.Mishra,A.Sharma
Key ref:
M.Yogavel et al. (2007). SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution. Acta Crystallogr D Biol Crystallogr, 63, 931-934. PubMed id: 17642520 DOI: 10.1107/S0907444907029174
Date:
29-May-07     Release date:   25-Mar-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
B2CP37  (B2CP37_9ROSA) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
152 a.a.
152 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.15.1.1  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444907029174 Acta Crystallogr D Biol Crystallogr 63:931-934 (2007)
PubMed id: 17642520  
 
 
SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution.
M.Yogavel, J.Gill, P.C.Mishra, A.Sharma.
 
  ABSTRACT  
 
Superoxide dismutase (SOD) from Potentilla atrosanguinea (Wall. ex. Lehm.) was crystallized using 20% PEG 3350 and 0.2 M ammonium iodide and diffraction data were collected to 2.36 A resolution using an in-house Cu Kalpha X-ray source. Analyses show that data with a redundancy of 3.2 were sufficient to determine the structure by the SAD technique using the iodine anomalous signal. This redundancy is lower than that in previous cases in which protein structures were determined using iodines for phasing and in-house copper X-ray sources. Cocrystallization of proteins with halide salts such as ammonium iodide in combination with copper-anode X-ray radiation can therefore serve as a powerful and easy avenue for structure solution.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Electron-density map at 2.36 Å resolution after refinement with REFMAC. The final 2F[o] - F[c] map is contoured at the 1.5 level.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 931-934) copyright 2007.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445234 M.Yogavel, S.Khan, T.K.Bhatt, and A.Sharma (2010).
Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states.
  Acta Crystallogr D Biol Crystallogr, 66, 584-592.
PDB codes: 3lmt 3lmu 3lmv
  20862217 T.E.Edwards, I.Phan, J.Abendroth, S.H.Dieterich, A.Masoudi, W.Guo, S.N.Hewitt, A.Kelley, D.Leibly, M.J.Brittnacher, B.L.Staker, S.I.Miller, W.C.Van Voorhis, P.J.Myler, and L.J.Stewart (2010).
Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head.
  PLoS One, 5, 0.
PDB codes: 3la9 3laa
18582473 P.Aravind, G.Wistow, Y.Sharma, and R.Sankaranarayanan (2008).
Exploring the limits of sequence and structure in a variant betagamma-crystallin domain of the protein absent in melanoma-1 (AIM1).
  J Mol Biol, 381, 509-518.
PDB code: 3cw3
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