1W5U

GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)

Summary for 1W5U

• Entry DOI: 10.2210/pdb1w5u/pdb
• Related: 1AL4 1ALX 1ALZ 1AV2 1BDW 1C4D 1GMK 1GRM 1JNO 1JO3 1JO4 1KQE 1MAG 1MIC 1NG8 1NRM 1NRU 1NT5 1NT6 1TK2 1TKQ 2IZQ 2XDC 3L8L
• Related PRD ID: PRD_000152
• Descriptor: GRAMICIDIN D, RUBIDIUM ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: antibiotic, gramicidin, antifungal, antibacterial, membrane ion channel, linear gramicidin
• Biological source: BACILLUS BREVIS; More
• Total number of polymer chains: 4
• Total formula weight: 8984.51

Authors

Glowka, M.L.,Olczak, A.,Bojarska, J.,Szczesio, M.,Duax, W.L.,Burkhart, B.M.,Pangborn, W.A.,Langs, D.A.,Wawrzak, Z. (deposition date: 2004-08-10, release date: 2005-09-15, Last modification date: 2023-12-13)

Primary citation

Glowka, M.L.,Olczak, A.,Bojarska, J.,Szczesio, M.,Duax, W.L.,Burkhart, B.M.,Pangborn, W.A.,Langs, D.A.,Wawrzak, Z.
Structure of Gramicidin D-Rbcl Complex at Atomic Resolution from Low-Temperature Synchrotron Data: Interactions of Double-Stranded Gramicidin Channel Contents and Cations with Channel Wall
Acta Crystallogr.,Sect.D, 61:433-, 2005

PubMed Abstract: Gramicidin D (gD) is a naturally occurring ionophoric antibiotic that forms membrane channels specific for monovalent cations. The crystal structure of the RbCl complex of gD has been determined at 1.14 A resolution from low-temperature (100 K) synchrotron-radiation data with a final R of 16%. The structure was refined with anisotropic temperature factors for all non-H atoms and with partial occupancies for many of them. The asymmetric unit in the crystal contains four crystallographically independent molecules that form two right-handed antiparallel double-stranded dimers. There are seven distinct rubidium-binding sites in each dimeric channel. The occupancy factors of Rb cations are between 0.11 and 0.35 and the total ion contents of the two crystallographically independent channels are 1.59 and 1.22 ions, respectively. Although each channel is 'chemically symmetrical', the side-chain conformations, the distributions of rubidium cations and their binding sites in the two independent channels are not. Cations are 'coordinated' by delocalized pi-electrons of three to five carbonyl groups that together with peptide backbone chains form the gramicidin channel walls. The water:cation ratio in the channel interior is four or five:one, and five or six waters separate Rb cations during their passage through the channel.

PubMed: 15805598
DOI: 10.1107/S0907444905000399

Experimental method

X-RAY DIFFRACTION (1.14 Å)