Computational protocol: Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease

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Protocol publication

[…] Diffraction data of GVE2 HNHE with Zn2+, Mn2+ and Hg-SAD were collected at the BL17U beamline of Shanghai Synchrotron Radiation Facility, the beamline BL1A and BL5A at the Photon Factory in Japan and the beamline 1W2B at Beijing Synchrotron Radiation Facility, respectively. Data were integrated and scaled with the HKL2000 package. The positions of heavy atoms and the initial phases of GVE2 HNHE were calculated by SAD using HKL2MAPand Phenix with a mercury derivative data set. The structure of GVE2 HNHE with Mn2+ was determined by molecular replacement with the Phaser programmer in the CCP4 programed suite. In addition, according to the anomalous difference Fourier maps calculated with a data set collected at a wavelength of 1.8 Å, the location of Mn2+ was confirmed. The structure refinements were carried out with Refmac and Phenix. Model building was carried out using Coot. MolProbity was used to validate the two structures. A summary of data collection and final refinement statistics are listed in .The program Pymol (http://www.pymol.org) was used to prepare the crystal structure figures of GVE2 HNHE. The sequence alignment figure () was prepared using ESPript. […]

Pipeline specifications

Software tools PHENIX, CCP4, Coot, MolProbity, PyMOL, ESPript
Application Protein structure analysis
Organisms Filamentous phage, Geobacillus virus E2
Chemicals Alanine