4UM4

STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH SULFATE

Summary for 4UM4

• Entry DOI: 10.2210/pdb4um4/pdb
• Descriptor: INORGANIC PYROPHOSPHATASE, SULFATE ION (3 entities in total)
• Functional Keywords: hydrolase
• Biological source: ESCHERICHIA COLI
• Cellular location: Cytoplasm : P0A7A9
• Total number of polymer chains: 3
• Total formula weight: 59473.78

Authors

Campos-Acevedo, A.A.,Rudino-Pinera, E. (deposition date: 2014-05-15, release date: 2014-11-26, Last modification date: 2024-01-10)

Primary citation

Campos-Acevedo, A.A.,Diaz-Vilchis, A.,Sotelo-Mundo, R.R.,Rudino-Pinera, E.
First attempts to crystallize a non-homogeneous sample of thioredoxin from Litopenaeus vannamei: What to do when you have diffraction data of a protein that is not the target?
Biochem Biophys Rep, 8:284-289, 2016

PubMed Abstract: The importance of sample homogeneity and purity in protein crystallization is essential to obtain high-quality diffracting crystals. Here, in an attempt to determine the crystal structure of thioredoxin 1 from whiteleg shrimp (Trx), we inadvertently crystallized the hexameric inorganic pyrophosphatase of (E-PPase) from a non-homogeneous sample product during the initial over-expression steps and partial purification of Trx. The structure determination and identification of the crystallized protein were derived from several clues: the failures in the Molecular Replacement (MR) trials using Trx coordinates as a search model, the unit cell parameters and space group determination, and essentially by the use of the program . After using the previously deposited E-PPase structure (PDB entry 1mjw) as a search model and the correct space group assignation, the MR showed an E-PPase complexed with SO with small changes in the sulfate ion binding region when it compares to previously deposited E-PPases in the PDB. This work stresses the importance of protein purity to avoid the risk of crystallizing a contaminant protein or how pure need to be a protein sample in order to increase the possibility to obtain crystals, but also serves as a reminder that crystallization is by itself a purification process and how the program can be useful in the crystal structure determination of previously deposited structures in the PDB.

PubMed: 28955968
DOI: 10.1016/j.bbrep.2016.09.011

Experimental method

X-RAY DIFFRACTION (2.65 Å)