wwPDB validation report of PDB entry 3KGW

Alanine-glyoxylate aminotransferase isoform CRA_b

THE SAME PROTEIN WITHOUT ENDOGENOUS PYRIDOXAL-5'-PHOSPHATE

THIS CONSTRUCT (RESIDUE 23-414) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 5. ELECTRON DENSITY IN THE ACTIVE SITE IS SOMEWHAT DISORDERED. TWO CONFORMERS ARE MODELED IN THIS REGION. THE CONFORMER A MODEL IS SIMILAR TO THE MODEL FROM THE RELATED STRUCTURE 3KGX. ENDOGENOUS PYRIDOXAL-5'-PHOSPHATE (PLP) IS MODELED IN EACH CHAIN IN THE B CONFORMER BASED ON THE ELECTRON DENSITY AND HOMOLOGY TO PDB 1H0C. THE OCCUPANCY OF PLP WAS REDUCED TO 0.5 TO BETTER MATCH THE OBSERVED DENSITY.

Crystal structure of Putative aminotransferase (AAH25799.1) from MUS MUSCULUS at 1.65 A resolution

CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

The largest off-origin peak in the Patterson function is 4.05% of the height of the origin peak. No significant pseudotranslation is detected.

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)