PDBsum entry 3a38

Go to PDB code: 
protein ligands links
Electron transport PDB id
Protein chain
83 a.a. *
SO4 ×3
Waters ×227
* Residue conservation analysis
PDB id:
Name: Electron transport
Title: Crystal structure of high-potential iron-sulfur protein from thermochromatium tepidum at 0.7 angstrom resolution
Structure: High-potential iron-sulfur protein. Chain: a. Synonym: hipip
Source: Thermochromatium tepidum. Chromatium tepidum. Organism_taxid: 1050
0.70Å     R-factor:   0.067     R-free:   0.075
Authors: K.Takeda,K.Kusumoto,Y.Hirano,K.Miki
Key ref: K.Takeda et al. (2010). Detailed assessment of X-ray induced structural perturbation in a crystalline state protein. J Struct Biol, 169, 135-144. PubMed id: 19782139
10-Jun-09     Release date:   26-Jan-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P80176  (HIP_THETI) -  High-potential iron-sulfur protein
83 a.a.
83 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     electron carrier activity     4 terms  


J Struct Biol 169:135-144 (2010)
PubMed id: 19782139  
Detailed assessment of X-ray induced structural perturbation in a crystalline state protein.
K.Takeda, K.Kusumoto, Y.Hirano, K.Miki.
The positions of hydrogen atoms significantly define protein functions. However, such information from protein crystals is easily disturbed by X-rays. The damage can not be prevented completely even in the data collection at cryogenic temperatures. Therefore, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. Diffraction data from a single crystal of the high-potential iron-sulfur protein (HiPIP) from Thermochromatium tepidum were collected at an undulator beamline of a third generation synchrotron facility, and were merged into three data sets according to X-ray dose. A series of structures analyzed at 0.70A shows detailed views of the X-ray induced perturbation, such as the positional changes of hydrogen atoms of a water molecule. Based on the results, we successfully collected a low perturbation data set using attenuated X-rays. There was no influence on the crystallographic statistics, such as the relative B factors, during the course of data collection. The electron densities for hydrogen atoms were more clear despite the slightly lower resolution.