1SMM

Crystal Structure of Cp Rd L41A mutant in oxidized state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer

Park, I.Y.Youn, B.Harley, J.L.Eidsness, M.K.Smith, E.Ichiye, T.Kang, C.

(2004) J Biol Inorg Chem 9: 423-428

  • DOI: 10.1007/s00775-004-0542-3
  • Primary Citation of Related Structures:  
    1SMM, 1SMU, 1SMW

  • PubMed Abstract: 
  • Rubredoxin is a small iron-sulfur (FeS4) protein involved in oxidation-reduction reactions. The side chain of Leu41 near the iron-sulfur center has two conformations, which we suggested previously serve as a gate for a water molecule during the electron transfer process ...

    Rubredoxin is a small iron-sulfur (FeS4) protein involved in oxidation-reduction reactions. The side chain of Leu41 near the iron-sulfur center has two conformations, which we suggested previously serve as a gate for a water molecule during the electron transfer process. To establish the role of residue 41 in electron transfer, an [L41A] mutant of Clostridium pasteurianum rubredoxin was constructed and crystallized in both oxidation states. Despite the lack of the gating side chain in this protein, the structure of the reduced [L41A] rubredoxin reveals a specific water molecule in the same position as observed in the reduced wild-type rubredoxin. In contrast, both the wild-type and [L41A] rubredoxins in the oxidized state do not have water molecules in this location. The reduction potential of the [L41A] variant was approximately 50 mV more positive than wild-type. Based on these observations, it is proposed that the site around the Sgamma of Cys9 serves as a port for an electron acceptor. Lastly, the Fe-S distances of the reduced rubredoxin are expanded, while the hydrogen bonds between Sgamma of the cysteines and the backbone amide nitrogens are shortened compared to its oxidized counterpart. This small structural perturbation in the Fe(II)/Fe(III) transition is closely related to the small energy difference which is important in an effective electron transfer agent.


    Organizational Affiliation

    School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RubredoxinA54Clostridium pasteurianumMutation(s): 1 
UniProt
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00268
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.788α = 90
b = 62.788β = 90
c = 32.797γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
CrystalCleardata reduction
AMoREphasing
X-PLORrefinement
CrystalCleardata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations