3L8L

Gramicidin D complex with sodium iodide

Summary for 3L8L

• Entry DOI: 10.2210/pdb3l8l/pdb
• Related: 1AL4 1ALX 1ALZ 1AV2 1BDW 1C4D 1GMK 1GRM 1JNO 1JO3 1JO4 1KQE 1MAG 1MIC 1NG8 1NRM 1NRU 1NT5 1NT6 1TK2 1TKQ 1W5U 2IZQ 2XDC
• Related PRD ID: PRD_000152
• Descriptor: GRAMICIDIN D, SODIUM ION, IODIDE ION, ... (6 entities in total)
• Functional Keywords: gramicidin, antifungal, antibacterial, antibiotic, membrane ion channel, linear gramicidin, gramicidin-nai complex
• Biological source: BACILLUS BREVIS; More
• Total number of polymer chains: 4
• Total formula weight: 8527.52

Authors

Olczak, A.,Glowka, M.L.,Szczesio, M.,Bojarska, J.,Wawrzak, Z.,Duax, W.L. (deposition date: 2009-12-31, release date: 2010-07-28, Last modification date: 2024-11-06)

Primary citation

Olczak, A.,Glowka, M.L.,Szczesio, M.,Bojarska, J.,Wawrzak, Z.,Duax, W.L.
The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex.
Acta Crystallogr.,Sect.D, 66:874-880, 2010

PubMed Abstract: The crystal structure of the nonstoichiometric complex of gramicidin D with NaI has been studied using synchrotron radiation at 100 K. The limiting resolution was 1.25 A and the R factor was 16% for 19 883 observed reflections. The general architecture of the antiparallel two-stranded gramicidin dimers in the studied crystal was a right-handed antiparallel double-stranded form that closely resembles the structures of other right-handed species published to date. However, there were several surprising observations. In addition to the significantly different composition of linear gramicidins identified in the crystal structure, including the absence of the gramicidin C form, only two cationic sites were found in each of the two independent dimers (channels), which were partially occupied by sodium, compared with the seven sites found in the RbCl complex of gramicidin. The sum of the partial occupancies of Na(+) was only 1.26 per two dimers and was confirmed by the similar content of iodine ions (1.21 ions distributed over seven sites), which was easily visible from their anomalous signal. Another surprising observation was the significant asymmetry of the distributions and occupancies of cations in the gramicidin dimers, which was in contrast to those observed in the high-resolution structures of the complexes of heavier alkali metals with gramicidin D, especially that of rubidium.

PubMed: 20693686
DOI: 10.1107/S0907444910019876

Experimental method

X-RAY DIFFRACTION (1.25 Å)