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PDBsum entry 1yk4

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protein metals links
Electron transport PDB id
1yk4
Jmol
Contents
Protein chain
52 a.a. *
Metals
_FE
Waters ×94
* Residue conservation analysis
PDB id:
1yk4
Name: Electron transport
Title: Ultra-high resolution structure of pyrococcus abyssi rubredoxin w4l/r5s
Structure: Rubredoxin. Chain: a. Synonym: rd. Engineered: yes. Mutation: yes
Source: Pyrococcus abyssi. Organism_taxid: 29292. Gene: rub. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
0.69Å     R-factor:   0.100     R-free:   0.108
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9V099  (RUBR_PYRAB) -  Rubredoxin
Seq:
Struc:
53 a.a.
52 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     3 terms  

 

 
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 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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20516622 A.Higashiura, T.Kurakane, M.Matsuda, M.Suzuki, K.Inaka, M.Sato, T.Kobayashi, T.Tanaka, H.Tanaka, K.Fujiwara, and A.Nakagawa (2010).
High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 698-708.
PDB code: 3klr
19997764 B.J.Goodfellow, I.C.Duarte, A.L.Macedo, B.F.Volkman, S.G.Nunes, I.Moura, J.L.Markley, and J.J.Moura (2010).
An NMR structural study of nickel-substituted rubredoxin.
  J Biol Inorg Chem, 15, 409-420.
PDB code: 2kkd
18814299 P.Labute (2009).
Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures.
  Proteins, 75, 187-205.  
17636129 G.Hagelueken, L.Wiehlmann, T.M.Adams, H.Kolmar, D.W.Heinz, B.Tümmler, and W.D.Schubert (2007).
Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa.
  Proc Natl Acad Sci U S A, 104, 12276-12281.
PDB codes: 2v3a 2v3b
17712580 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2007).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O-H...Sgamma-Fe hydrogen bond increased the reduction potential by 65 mV.
  J Biol Inorg Chem, 12, 1163-1171.
PDB code: 2pya
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