2IZQ

Gramicidin D complex with KI

Summary for 2IZQ

• Entry DOI: 10.2210/pdb2izq/pdb
• Related: 1AL4 1ALX 1ALZ 1AV2 1BDW 1C4D 1GMK 1GRM 1JNO 1JO3 1JO4 1KQE 1MAG 1MIC 1NG8 1NRM 1NRU 1NT5 1NT6 1TK2 1TKQ 1W5U 2XDC 3L8L
• Related PRD ID: PRD_000152
• Descriptor: GRAMICIDIN D, POTASSIUM ION, IODIDE ION, ... (5 entities in total)
• Functional Keywords: antibiotic, gramicidin, antifungal, antibacterial, membrane ion channel, linear gramicidin
• Biological source: BREVIBACILLUS BREVIS
• Total number of polymer chains: 4
• Total formula weight: 9003.29

Authors

Olczak, A.,Glowka, M.L.,Szczesio, M.,Bojarska, J.,Duax, W.L.,Burkhart, B.M.,Wawrzak, Z. (deposition date: 2006-07-26, release date: 2007-01-23, Last modification date: 2024-11-06)

Primary citation

Olczak, A.,Glowka, M.L.,Szczesio, M.,Bojarska, J.,Duax, W.L.,Burkhart, B.M.,Wawrzak, Z.
Nonstoichiometric Complex of Gramicidin D with Ki at 0.80 A Resolution.
Acta Crystallogr.,Sect.D, 63:319-, 2007

PubMed Abstract: The crystal structure of a nonstoichiometric complex of gramicidin D (gD) with KI has been determined at 100 K using synchrotron radiation. The final R factor was 0.106 for 83 988 observed reflections (Friedel pairs were not merged) collected to 0.80 A. The structure consists of four independent pentadecapeptides and numerous solvent molecules and salt ions. The general architecture of the antiparallel double-stranded gramicidin dimers in the crystal (a right-handed antiparallel DSbetaH(R) form) closely resembles that of previously published cation complexes of gD. However, a significantly different mixture of gramicidin isomers is found in the crystal of the KI complex, including partial occupancy of phenylalanine at position 11. Only three sites in each of the two crystallographically independent channels are partially occupied by potassium cations instead of the commonly observed seven sites. The sum of the partial occupancies of K(+) (1.10 per two dimers) is consistent with the sum of the iodide occupancies (1.095 over eight sites), which is also confirmed by the anomalous signal of the iodide. There was a significant asymmetry of the distribution and occupancies of cations in the crystallographically independent gramicidin channels, in contrast to the distribution found in the rubidium chloride complex with gD.

PubMed: 17327669
DOI: 10.1107/S0907444906053649

Experimental method

X-RAY DIFFRACTION (0.8 Å)