wwPDB validation report of PDB entry 3N1L

Crystal Structure of StWhy2-ERE32 complex

Crystal Structure of StWhy2-dT32 complex

Crystal Structure of StWhy2-cERE32 complex

THE SEQUENCE OF THE CRYSTALLIZED DNA IS A 32-MER OLIGONUCLEOTIDE WITH SEQUENCE ACAGTAAAAACAGTAAAAACAGTAAAAACAGT. ONLY 9 RESIDUES OF DEOXYADENOSINE WERE MODELED IN THE COORDINATES OF THE ASYMMETRIC UNIT. ACCORDING TO THE AUTHORS, THE 32-MER DNA BINDS A TETRAMER THAT INCLUDE FOUR MONOMERS OF FOUR ASYMMETRIC UNITS; THE STWHY2-DNA BINDING IS NOT SEQUENCE SPECIFIC THUS EACH TETRAMERIC PROTEIN BINDS A 32-MER DNA IN DIFFERENT SEQUENCE REGISTERS; AS A RESULT ONLY THREE OF THE FOUR DNA-BINDING SITES OF EACH TETRAMER WOULD BE PHYSICALLY OCCUPIED BY THE DNA.

Crystal Structure of a StWhy2-rcERE32 complex

Authors state that the biological unit is a tetramer protein plus a 32-mer DNA molecule, as indicated as pentamer in remark 350. Please refer to remark 999 for more details on the sequences specificity of this crystal structure.

The largest off-origin peak in the Patterson function is 4.40% 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)