PDBsum entry 1yk5

Electron transport

PDB id: 1yk5

Contents

Protein chains

53 a.a. *

Metals

_FE ×4

Waters ×157

* Residue conservation analysis

PDB id:

1yk5

Name:

Electron transport

Title:

Pyrococcus abyssi rubredoxin

Structure:

Rubredoxin. Chain: a, b, c, d. Synonym: rd. Engineered: yes

Source:

Pyrococcus abyssi. Organism_taxid: 29292. Gene: rub. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.79Å R-factor: 0.158 R-free: 0.191

Authors:

H.Bonisch,C.L.Schmidt,P.Bianco,R.Ladenstein

Key ref:

H.Bönisch et al. (2005). Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S. Acta Crystallogr D Biol Crystallogr, 61, 990. PubMed id: 15983423 DOI: 10.1107/S090744490501293X

Date:

17-Jan-05 Release date: 17-Jan-06

Protein chains

Q9V099  (RUBR_PYRAB) -  Rubredoxin from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 53 a.a.

Struc: 53 a.a.

DOI no: 10.1107/S090744490501293X

Acta Crystallogr D Biol Crystallogr 61:990 (2005)

PubMed id: 15983423

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.

H.Bönisch, C.L.Schmidt, P.Bianco, R.Ladenstein.

ABSTRACT

The crystal structure of Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved by direct methods. The model of the air-oxidized protein was refined by partially restrained full-matrix least-squares refinement against intensity data to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin provides very detailed and precise information about the Fe(SCys)(4) centre and its environment, the peptide-backbone stereochemistry, H atoms and hydrogen bonds, static and dynamic disorder, the solvent structure and the electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a series of mutants studied by atomic and ultrahigh-resolution X-ray crystallography which are expected to contribute to the understanding of structure-function relationships in iron-sulfur proteins.

Selected figure(s)

Figure 3.
Figure 3 P. abyssi rubredoxin W4L/R5S. Electron-density maps calculated from the final model refined to 0.69 Å resolution, superimposed onto the final model. (a) 2mF[o] - DF[c] difference map of the redox centre; the contour level is 3.0 [sigma] . (b) 2mF[o] - DF[c] difference map (white; contour level 3.0 [sigma] ) and proton-omit map (cyan; contour level 2.0 [sigma] ) of the antiparallel [beta] -sheet. The main chain of the final model is shown. D-H [\cdots] A and C-H [\cdots] O hydrogen bonds are marked by red lines. (c) 2mF[o] - DF[c] difference map (white; contour level 3.0 [sigma] ) and proton omit map (cyan; contour level 2.0 [sigma] ) of a hydrogen-bond network with well ordered solvent molecules. The hydrogen bonds are marked by red lines. (d) 2mF[o] - DF[c] difference map (white; contour level 3.0 [sigma] ) and mF[o] - DF[c] difference map (green; contour level 2.0 [sigma] ) for residues Asp14-Asp19 and Ser25-Thr28. The main chain of the final model is shown.

Figure 4.
Figure 4 P. abyssi rubredoxin wild-type molecule A (cyan) and mutant W4L/R5S (atom colours). Superposition of the Fe(SCys)[4] site.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 990-0) copyright 2005.

Figures were selected by the author.