Computational protocol: Tail tubular protein A: a dual-function tail protein of Klebsiella pneumoniae bacteriophage KP32

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Protocol publication

[…] We used the amino acid sequence of TTPA to search all structures deposited in the Protein Data Bank (PDB) using the molecular replacement method, but found no potential structural model that could be used to solve the crystal structure of TTPA. Thus, we obtained the Se-Met derivative crystals of TTPA and used them to solve the crystal structure with the SHELXD/E programs. The protein polypeptide chain was built into an electron density map using the wARP/ARP program. Refinement and water selection were performed with REFMAC5 in the CCP4i package, . Real-space model corrections were performed with Coot. The structure quality was validated with PROCHECK. The figures representing the crystal structures were prepared in Coot or PyMol. The coordinates and structural factors were deposited in PDB and assigned the accession code, 5MU4. […]

Pipeline specifications

Software tools SHELX, REFMAC5, Coot, PROCHECK, PyMOL
Application Protein structure analysis
Organisms Dipturus trachyderma, Enterobacteria phage T7, Salmonella virus P22
Diseases Pneumonia
Chemicals Amino Acids