1VCX

Neutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution

Summary for 1VCX

• Entry DOI: 10.2210/pdb1vcx/pdb
• Descriptor: Rubredoxin, FE (III) ION (3 entities in total)
• Functional Keywords: neutron structure, hydrogen atom position, hydration water structure, hydrogen/deuterium exchange, iron-sulfur core, n-terminal region, electron transport
• Biological source: Pyrococcus furiosus
• Total number of polymer chains: 1
• Total formula weight: 5956.38

Authors

Kurihara, K.,Tanaka, I.,Chatake, T.,Adams, M.W.W.,Jenney Jr., F.E.,Moiseeva, N.,Bau, R.,Niimura, N. (deposition date: 2004-03-17, release date: 2004-08-10, Last modification date: 2024-12-25)

Primary citation

Kurihara, K.,Tanaka, I.,Chatake, T.,Adams, M.W.W.,Jenney Jr., F.E.,Moiseeva, N.,Bau, R.,Niimura, N.
Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules
Proc.Natl.Acad.Sci.USA, 101:11215-11220, 2004

PubMed Abstract: The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.

PubMed: 15272083
DOI: 10.1073/pnas.0403807101

Experimental method

NEUTRON DIFFRACTION (1.5 Å)