3PDI

Precursor bound NifEN

• PDB DOI:  https://doi.org/10.2210/pdb3PDI/pdb

• Classification: PROTEIN BINDING
• Organism(s): Azotobacter vinelandii DJ
• Expression System: Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2010-10-22 Released: 2011-01-19 
• Deposition Author(s): Kaiser, J.T., Hu, Y., Wiig, J.A., Rees, D.C., Ribbe, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.341 
• R-Value Work: 0.294 
• R-Value Observed: 0.299 

Literature

Structure of Precursor-Bound NifEN: A Nitrogenase FeMo Cofactor Maturase/Insertase.

Kaiser, J.T., Hu, Y., Wiig, J.A., Rees, D.C., Ribbe, M.W.

(2011) Science 331: 91-94

• PubMed: 21212358 
• DOI: https://doi.org/10.1126/science.1196954
• Primary Citation of Related Structures:  
  3PDI


• PubMed Abstract: 
  

NifEN plays an essential role in the biosynthesis of the nitrogenase iron-molybdenum (FeMo) cofactor (M cluster). It is an α(2)β(2) tetramer that is homologous to the catalytic molybdenum-iron (MoFe) protein (NifDK) component of nitrogenase. NifEN serves as a scaffold for the conversion of an iron-only precursor to a matured form of the M cluster before delivering the latter to its target location within NifDK. Here, we present the structure of the precursor-bound NifEN of Azotobacter vinelandii at 2.6 angstrom resolution. From a structural comparison of NifEN with des-M-cluster NifDK and holo NifDK, we propose similar pathways of cluster insertion for the homologous NifEN and NifDK proteins.

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Organizational Affiliation: 

Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA.

Biological Assembly 1  

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)

Biological Assembly 2  

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 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 413.77 kDa 
• Atom Count: 26,112 
• Modelled Residue Count: 3,436 
• Deposited Residue Count: 3,764 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase MoFe cofactor biosynthesis protein NifE	A, C, E, G	483	Azotobacter vinelandii DJ	Mutation(s): 0  Gene Names: Avin_01450, nifE
UniProt
Find proteins for C1DH03 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DH03  Go to UniProtKB:  C1DH03

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase MoFe cofactor biosynthesis protein NifN	B, D, F, H	458	Azotobacter vinelandii DJ	Mutation(s): 0  Gene Names: Avin_01470, nifN
UniProt
Find proteins for C1DH04 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DH04  Go to UniProtKB:  C1DH04

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CZL	J [auth A], L [auth C], N [auth E], P [auth G]	L-Cluster (Fe8S9) Fe8 H6 S9 FRFZBLMXGBLMJN-UHFFFAOYSA-N
SF4	I [auth A], K [auth C], M [auth E], O [auth G]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.341 
• R-Value Work: 0.294 
• R-Value Observed: 0.299 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.07	α = 90
b = 95.22	β = 95.5
c = 149.98	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Kaiser, J.T., Hu, Y., Wiig, J.A., Rees, D.C., Ribbe, M.W.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance