PDBsum entry 1vcx

Electron transport

PDB id: 1vcx

Contents

Protein chain

53 a.a. *

Ligands

DOD ×37

Metals

_FE

* Residue conservation analysis

PDB id:

1vcx

Name:

Electron transport

Title:

Neutron crystal structure of the wild type rubredoxin from pyrococcus furiosus at 1.5a resolution

Structure:

Rubredoxin. Chain: a. Synonym: pf rd. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Authors:

K.Kurihara,I.Tanaka,T.Chatake,M.W.W.Adams,F.E.Jenney Jr.,N.Moiseeva, R.Bau,N.Niimura

Key ref:

K.Kurihara et al. (2004). Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules. Proc Natl Acad Sci U S A, 101, 11215-11220. PubMed id: 15272083 DOI: 10.1073/pnas.0403807101

Date:

17-Mar-04 Release date: 10-Aug-04

Protein chain

P24297  (RUBR_PYRFU) -  Rubredoxin from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 54 a.a.

Struc: 53 a.a.

DOI no: 10.1073/pnas.0403807101

Proc Natl Acad Sci U S A 101:11215-11220 (2004)

PubMed id: 15272083

Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules.

K.Kurihara, I.Tanaka, T.Chatake, M.W.Adams, F.E.Jenney, N.Moiseeva, R.Bau, N.Niimura.

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.

Selected figure(s)

Figure 3.
Fig. 3. Examples of the hydration water molecules. (a) F[o] - F[c] omit map (at 4.0 ) of the hydration water molecules near the residues Gly-9 and Ser-46 of a neighboring molecule. Note the presence of two types of water molecules. Water #3 has a triangular shape and is fully ordered, whereas water #4 has an ellipsoidal shape and is only partially ordered with only one D atom (cyan) and one O atom (red) visible. The third atom (D) of water #4 is rotationally disordered and is not observable in this map. (b) F[o] - F[c] omit map at 4.0 level of the hydration water molecule (#7) near Asp-18 and Asp-20. The green line corresponds to a previously suspected H bond whose existence has been disproved on the basis of neutron data (see text). The dotted lines indicate H bonds.

Figure 5.
Fig. 5. F[o] - F[c] omit map showing the "arc" of H bonds around the N-terminal region of WT rubredoxin. Contouring level is 3.0 , and H bonds are shown as dotted lines. Note that the high resolution of this map allows all three D atoms of this group to be resolved.

Figures were selected by an automated process.