wwPDB validation report of PDB entry 3TY9

Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase

Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (E.C.6.5.1.3)
Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate

PROTEIN IS KNOWN TO FORM A DIMER WHICH INTERACTS WITH A DIMER OF HEN1 TO GIVE A HETEREOTETRAMER (2-PNKP/2-HEN1). THE OLIGOMERIC ORGANIZATIONS PRESENT IN THE CRYSTAL ARE ENUMERATED BELOW BUT MAY NOT CORRESPOND TO ANY OLIGOMER PRESENT IN THE HEN1/PNKP HETERODIMER

The analyses of the Patterson function reveals a significant off-origin peak that is 38.51 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 3.6497e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.

structure factor analysis and validation
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)