Virulence-associated proteins (Vaps) have been found in many organisms, but as yet little is known about their structure and function. There is an evidence suggesting that Vaps should be related to CAS2 family of ribonucleases associated with the CRISPR system of microbial immunity. Here we report a crystal structure of the 16.3 kDa VapD protein from the phytopathogen Xylella fastidiosa. Crystals were grown by the hanging drop method by mixing 1.8 ll of a protein solution (9.8 mg/ml) with an equal amount of 20% (v/v) MPD and 0.1 M glycine in 0.1 M NaOAc, pH 4.5. Diffraction data were collected at a wavelength of 1.46 A using MAR Mosaic CCD 225 detector on the W01B- MX2 beamline of the Brazilian Synchrotron Light Laboratory. Crystals were found to be immanent merohedral twins with a twinning fraction of 0.48. In spite of the lack of suitable sequence homology, a successful solution was found by the molecular replacement method with a search model prepared ab initio using the ROSETTA suite. The refined protein model confirms the accuracy and reliability of the solution found, with R-factor and R-free values equal to 0.250 and 0.308, respectively. In order to elucidate a possible mechanism of action, a search for structural analogous was carried out in PDB. Structural alignment using DALI revealed a probable DNA binding cleft on the surface of the protein. Computer molecular dynamics simulation with GROMACS has proved a stability of the suggested DNA-protein complex. The refined model furnished structural details which may provide an important evidence for the VapD function.