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PDBsum entry 1iu5

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protein ligands metals links
Electron transport PDB id
1iu5
Jmol
Contents
Protein chain
51 a.a. *
Ligands
DOD ×53
Metals
_FE
* Residue conservation analysis
PDB id:
1iu5
Name: Electron transport
Title: X-ray crystal structure of the rubredoxin mutant from pyroco furiosus
Structure: Rubredoxin. Chain: a. Engineered: yes. Mutation: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.50Å     R-factor:   0.187     R-free:   0.203
Authors: T.Chatake,K.Kurihara,I.Tanaka,I.Tsyba,R.Bau,F.E.Jenney,M.W.W N.Niimura
Key ref:
T.Chatake et al. (2004). A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution. Acta Crystallogr D Biol Crystallogr, 60, 1364-1373. PubMed id: 15272158 DOI: 10.1107/S090744490401176X
Date:
27-Feb-02     Release date:   27-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24297  (RUBR_PYRFU) -  Rubredoxin
Seq:
Struc:
54 a.a.
51 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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/S090744490401176X Acta Crystallogr D Biol Crystallogr 60:1364-1373 (2004)
PubMed id: 15272158  
 
 
A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution.
T.Chatake, K.Kurihara, I.Tanaka, I.Tsyba, R.Bau, F.E.Jenney, M.W.Adams, N.Niimura.
 
  ABSTRACT  
 
A neutron diffraction study has been carried out at 1.6 A resolution on a mutant rubredoxin from Pyrococcus furiosus using the BIX-3 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Research Institute. In order to study the unusual thermostability of rubredoxin from P. furiosus (an organism that grows optimally at 373 K), the hydrogen-bonding patterns were compared between the wild-type protein and a 'triple-mutant' variant. In this mutant protein, three residues were changed (Trp3-->Tyr3, Ile23-->Val23, Leu32-->Ile32) so that they are identical to those in a mesophilic rubredoxin from Clostridium pasteurianum. In the present study, some minor changes were found between the wild-type and mutant proteins in the hydrogen-bonding patterns of the Trp3/Tyr3 region. In this investigation, the H/D-exchange ratios in the protein were also studied. Because the target protein was soaked in D2O during the crystallization procedure, most of the N-H and O-H bonds have become deuterated, while essentially all of the C-H bonds have not. In particular, the H/D-exchange pattern of the N-H amide bonds of the protein backbone is of interest because it may contain some indirect information about the mechanism of unfolding of this small protein. The results are in broad agreement with those from solution NMR studies, which suggest that the backbone amide bonds near the four Cys residues of the FeS4 redox center are most resistant to H/D exchange. Finally, the detailed geometries of the water molecules of hydration around the rubredoxin molecule are also reported. The 1.6 A resolution of the present neutron structure determination has revealed a more detailed picture than previously available of some portions of the water structure, including ordered and disordered O-D bonds. Crystallographic details: space group P2(1)2(1)2(1) (orthorhombic), unit-cell parameters a = 34.48, b = 35.70, c = 43.16 A; final agreement factors R = 0.196 and Rfree = 0.230 for 19,384 observed and 6548 unique neutron reflections collected at room temperature; crystal size 4 mm3; a total of 423 non-H atoms, 290 H atoms and 88 D atoms were located in this study.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 A final refined 2|F[o]| - |F[c]| neutron density map superimposed on the Trp36 residue. Blue and red contours show positive and negative densities, respectively. The green broken line shows a hydrogen bond between the N-D bond of Trp36 and the carboxyl group of Glu18. Note the positive contours of the N-D group and the entire D[2]O molecule, as opposed to the negative contours of the H atoms of the C-H bonds.
Figure 6.
Figure 6 Maps around the third mutated region: (a) Trp3 in wild-type PfRd (Kurihara et al., 2001[Kurihara, K., Tanaka, I., Adams, M. W. W., Jenney, F. E. Jr, Moiseeva, N., Bau, R. & Niimura, N. (2001). J. Phys. Soc. Jpn Suppl. A, 70, 400-402.]) and (b) Tyr3 in mut-PfRd. The black and red broken lines show strong and weak hydrogen bonds, respectively. The blue contours correspond to positive neutron density regions. Note that Trp3 and Glu14 are directly hydrogen bonded in PfRd (a), whereas in mut-PfRd there is no direct hydrogen bond between Tyr3 and Glu14 (b).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1364-1373) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19255494 W.R.Novak, A.G.Moulin, M.P.Blakeley, I.Schlichting, G.A.Petsko, and D.Ringe (2009).
A preliminary neutron diffraction study of gamma-chymotrypsin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 317-320.  
18656544 M.P.Blakeley, P.Langan, N.Niimura, and A.Podjarny (2008).
Neutron crystallography: opportunities, challenges, and limitations.
  Curr Opin Struct Biol, 18, 593-600.  
18156668 N.Niimura, and R.Bau (2008).
Neutron protein crystallography: beyond the folding structure of biological macromolecules.
  Acta Crystallogr A, 64, 12-22.  
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