1G5P

NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII

• PDB DOI: https://doi.org/10.2210/pdb1G5P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2000-11-01 Released: 2001-01-31 
• Deposition Author(s): Strop, P., Takahara, P.M., Chiu, H.J., Angove, H.C., Burgess, B.K., Rees, D.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.223 

Starting Model: experimental

Literature

Crystal structure of the all-ferrous [4Fe-4S]0 form of the nitrogenase iron protein from Azotobacter vinelandii.

Strop, P., Takahara, P.M., Chiu, H., Angove, H.C., Burgess, B.K., Rees, D.C.

(2001) Biochemistry 40: 651-656

• PubMed: 11170381 
• DOI: https://doi.org/10.1021/bi0016467
• Primary Citation of Related Structures:  
  1G1M, 1G5P


• PubMed Abstract: 
  

  The structure of the nitrogenase iron protein from Azotobacter vinelandii in the all-ferrous [4Fe-4S](0) form has been determined to 2.25 A resolution by using the multiwavelength anomalous diffraction (MAD) phasing technique. The structure demonstrates that major conformational changes are not necessary either in the iron protein or in the cluster to accommodate cluster reduction to the [4Fe-4S](0) oxidation state. A survey of [4Fe-4S] clusters coordinated by four cysteine ligands in proteins of known structure reveals that the [4Fe-4S] cluster of the iron protein has the largest accessible surface area, suggesting that solvent exposure may be relevant to the ability of the iron protein to exist in three oxidation states.

---

Organizational Affiliation: 

Biochemistry Option, California Institute of Technology, Mail Code 147-75, Pasadena, California 91125, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 63.19 kDa 
• Atom Count: 4,707 
• Modelled Residue Count: 575 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.12	α = 90
b = 90.53	β = 90
c = 91.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-31 
Deposition Author(s): Strop, P., Takahara, P.M., Chiu, H.J., Angove, H.C., Burgess, B.K., Rees, D.C.

Revision History  

• Version 1.0: 2001-01-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description