Primary Citation PubMed: 16306995
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PDA: an automatic and comprehensive analysis program for protein-DNA complex structures.
(2009) BMC Genomics 10 Suppl 1
PubMed: 19594872 | PubMedCentral: PMC2709256 | DOI: 10.1186/1471-2164-10-S1-S13
(C) The dimer of P1 ParB fragments of plasmid partition par B protein ( 1ZX4 ) has two different DNA binding domains.
The PDB file of 1ZX4 has the coordinates for one protein dimer and one double-stranded DNA.
However, in the original literature for 1ZX4 [ 31 ], three copies of the double-stranded DNA were shown to bind to the same protein dimer (on two different DNA binding domains).
Using the crystal symmetry information, PDA reconstructed the coordinates of the whole protein-DNA complex structure of 1ZX4 as reported [ 31 ].
The protein-DNA complex structure 1ZX4 is such an example, in which the protein has two different DNA binding domains (Figure 2C ).
(A) Restoration of "biological molecules" ( 1AN2 ); (B) Reconstruction of double-stranded DNAs ( 2IIE ); (C) Reconstruction of missing double-stranded DNAs ( 1ZX4 ); and (D) Identification of protein-DNA binding units ( 1A02 ).
Publication Year: 2009
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