Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.72 kDa 
• Atom Count: 997 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

1D3W

Crystal structure of ferredoxin 1 d15e mutant from azotobacter vinelandii at 1.7 angstrom resolution.

• PDB DOI: 10.2210/pdb1D3W/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Azotobacter vinelandii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-10-01 Released: 1999-10-14 
• Deposition Author(s): Chen, K., Hirst, J., Camba, R., Bonagura, C.A., Stout, C.D., Burges, B.K., Armstrong, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Atomically defined mechanism for proton transfer to a buried redox centre in a protein.

Chen, K., Hirst, J., Camba, R., Bonagura, C.A., Stout, C.D., Burgess, B.K., Armstrong, F.A.

(2000) Nature 405: 814-817

• PubMed: 10866206 
• DOI: 10.1038/35015610
• Primary Citation of Related Structures:  
  1D3W


• PubMed Abstract: 
  

The basis of the chemiosmotic theory is that energy from light or respiration is used to generate a trans-membrane proton gradient. This is largely achieved by membrane-spanning enzymes known as 'proton pumps. There is intense interest in experiments which reveal, at the molecular level, how protons are drawn through proteins. Here we report the mechanism, at atomic resolution, for a single long-range electron-coupled proton transfer. In Azotobacter vinelandii ferredoxin I, reduction of a buried iron-sulphur cluster draws in a solvent proton, whereas re-oxidation is 'gated' by proton release to the solvent. Studies of this 'proton-transferring module' by fast-scan protein film voltammetry, high-resolution crystallography, site-directed mutagenesis and molecular dynamics, reveal that proton transfer is exquisitely sensitive to the position and pK of a single amino acid. The proton is delivered through the protein matrix by rapid penetrative excursions of the side-chain carboxylate of a surface residue (Asp 15), whose pK shifts in response to the electrostatic charge on the iron-sulphur cluster. Our analysis defines the structural, dynamic and energetic requirements for proton courier groups in redox-driven proton-pumping enzymes.

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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, University of California, Irvine 92612, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERREDOXIN 1	A	106	Azotobacter vinelandii	Mutation(s): 1  Gene Names: fdxA
UniProt
Find proteins for P00214 (Azotobacter vinelandii) Explore P00214  Go to UniProtKB:  P00214

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
F3S	C [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.37	α = 90
b = 55.37	β = 90
c = 92.535	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-01 
• Released Date: 1999-10-14 
Deposition Author(s): Chen, K., Hirst, J., Camba, R., Bonagura, C.A., Stout, C.D., Burges, B.K., Armstrong, F.A.

Revision History  

• Version 1.0: 1999-10-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance