Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 232658.83 
• Atom Count: 15863 
• Residue Count: 2026 
• Unique protein chains: 2

3MIN

NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII, OXIDIZED STATE

• DOI: 10.2210/pdb3MIN/pdb

• Classification: NITROGEN FIXATION
• Organism(s): Azotobacter vinelandii


• Deposited: 1996-12-20 Released: 1997-04-01 
• Deposition Author(s): Peters, J.W., Stowell, M.H.B., Soltis, S.M., Day, M.W., Kim, J., Rees, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.264 
• R-Value Work: 0.206 

Literature

Redox-dependent structural changes in the nitrogenase P-cluster.

Peters, J.W., Stowell, M.H., Soltis, S.M., Finnegan, M.G., Johnson, M.K., Rees, D.C.

(1997) Biochemistry 36: 1181-1187

• PubMed: 9063865 
• DOI: 10.1021/bi9626665
• Primary Citation of Related Structures:  
  2MIN


• PubMed Abstract: 
  

The structure of the nitrogenase MoFe-protein from Azotobacter vinelandii has been refined to 2.0 A resolution in two oxidation states. EPR studies on the crystals indicate that the structures correspond to the spectroscopically assigned oxidized (P(OX)/M(OX)) and the native or dithionite-reduced (P(N)/M(N)) forms of the enzyme. Both MoFe-protein structures are essentially identical, with the exception of the P-cluster. The MoFe-protein P-cluster in each state is found to contain eight Fe and seven S atoms. Interconversion between the two redox states involves movement of two Fe atoms and an exchange of protein coordination for ligands supplied by a central S atom. In the oxidized P(OX) state, the cluster is coordinated by the protein through six cysteine ligands, Ser-beta188 O gamma, and the backbone amide of Cys-alpha88. In the native P(N) state, Ser-beta188 O gamma and the amide N of Cys-alpha88 no longer coordinate the cluster due to movement of their coordinated Fe atoms toward the central sulfur. Consequently, this central sulfur adopts a distorted octahedral environment with six surrounding Fe atoms. A previously described model of the P-cluster containing 8Fe-8S likely reflects the inappropriate modeling of a single structure to a mixture of these two P-cluster redox states. These observed redox-mediated structural changes of the P-cluster suggest a role for this cluster in coupling electron transfer and proton transfer in nitrogenase.

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Related Citations: 

• Structural Models for the Metal Centers in the Nitrogenase Molybdenum-Iron Protein
  Kim, J.,Rees, D.C.
  (1992) Science 257: 1677
• Crystallographic Structure and Functional Implications of the Nitrogenase Molybdenum-Iron Protein from Azotobacter Vinelandii
  Kim, J.,Rees, D.C.
  (1992) Nature 360: 553




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Organizational Affiliation: 

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NITROGENASE MOLYBDENUM IRON PROTEIN	A, C	491	Azotobacter vinelandii	Mutation(s): 0  Gene Names: nifD EC: 1.18.6.1
Find proteins for P07328 (Azotobacter vinelandii) Go to UniProtKB:  P07328

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
NITROGENASE MOLYBDENUM IRON PROTEIN	B, D	522	Azotobacter vinelandii	Mutation(s): 0  Gene Names: nifK EC: 1.18.6.1
Find proteins for P07329 (Azotobacter vinelandii) Go to UniProtKB:  P07329

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CFM	A, C	FE-MO-S CLUSTER Fe7 Mo S9 UZRXIPMKRKMLQF-VGXFRCDIAP
CA	B, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CLF	B, D	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-DHHOTQGYAO
HCA	A, C	3-HYDROXY-3-CARBOXY-ADIPIC ACID C7 H10 O7 XKJVEVRQMLKSMO-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.264 
• R-Value Work: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 108.000	α = 90.00
b = 131.300	β = 110.70
c = 81.000	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-12-20 
• Released Date: 1997-04-01 
• Deposition Author(s): Peters, J.W., Stowell, M.H.B., Soltis, S.M., Day, M.W., Kim, J., Rees, D.C.

Revision History 

• Version 1.0: 1997-04-01
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance