Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 63661.54 
• Atom Count: 4147 
• Residue Count: 578 
• Unique protein chains: 1

1NIP

CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII

• DOI: 10.2210/pdb1NIP/pdb

• Classification: IRON PROTEIN
• Organism(s): Azotobacter vinelandii


• Deposited: 1992-09-29 Released: 1993-10-31 
• Deposition Author(s): Komiya, H., Georgiadis, M.M., Chakrabarti, P., Woo, D., Kornuc, J.J., Rees, D.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å

Literature

Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii.

Georgiadis, M.M., Komiya, H., Chakrabarti, P., Woo, D., Kornuc, J.J., Rees, D.C.

(1992) Science 257: 1653-1659

• PubMed: 1529353 


• PubMed Abstract: 
  

The nitrogenase enzyme system catalyzes the ATP (adenosine triphosphate)-dependent reduction of dinitrogen to ammonia during the process of nitrogen fixation. Nitrogenase consists of two proteins: the iron (Fe)-protein, which couples hydrolysis of ATP to electron transfer, and the molybdenum-iron (MoFe)-protein, which contains the dinitrogen binding site. In order to address the role of ATP in nitrogen fixation, the crystal structure of the nitrogenase Fe-protein from Azotobacter vinelandii has been determined at 2.9 angstrom (A) resolution. Fe-protein is a dimer of two identical subunits that coordinate a single 4Fe:4S cluster. Each subunit folds as a single alpha/beta type domain, which together symmetrically ligate the surface exposed 4Fe:4S cluster through two cysteines from each subunit. A single bound ADP (adenosine diphosphate) molecule is located in the interface region between the two subunits. Because the phosphate groups of this nucleotide are approximately 20 A from the 4Fe:4S cluster, it is unlikely that ATP hydrolysis and electron transfer are directly coupled. Instead, it appears that interactions between the nucleotide and cluster sites must be indirectly coupled by allosteric changes occurring at the subunit interface. The coupling between protein conformation and nucleotide hydrolysis in Fe-protein exhibits general similarities to the H-Ras p21 and recA proteins that have been recently characterized structurally. The Fe-protein structure may be relevant to the functioning of other biochemical energy-transducing systems containing two nucleotide-binding sites, including membrane transport proteins.

---

Related Citations: 

• Crystal Structure of the Nitrogenase Iron Protein from Azotobacter Vinelandii
  Georgiadis, M.M.,Chakrabarti, P.,Rees, D.C.
  (1990) Nitrogen Fixation: Achievements and Objectives --: 1




---

Organizational Affiliation: 

Department of Biochemistry, Columbia University, New York, NY 10032.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NITROGENASE IRON PROTEIN	A, B	289	Azotobacter vinelandii	Mutation(s): 0  Gene Names: nifH1 EC: 1.18.6.1
Find proteins for P00459 (Azotobacter vinelandii) Go to UniProtKB:  P00459

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SF4	B	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
ADP	B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 56.800	α = 90.00
b = 92.900	β = 100.00
c = 63.600	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1992-09-29 
• Released Date: 1993-10-31 
• Deposition Author(s): Komiya, H., Georgiadis, M.M., Chakrabarti, P., Woo, D., Kornuc, J.J., Rees, D.C.

Revision History 

• Version 1.0: 1993-10-31
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance