Biological Assembly 1  

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

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: 222.31 kDa 
• Atom Count: 18065 
• Modelled Residue Count: 1953 
• Deposited Residue Count: 1984 
• Unique protein chains: 2

4WES

Nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 1.08 A resolution

• PDB DOI: 10.2210/pdb4WES/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium pasteurianum DSM 525 = ATCC 6013
• Mutation(s): No 


• Deposited: 2014-09-10 Released: 2015-02-11 
• Deposition Author(s): Zhang, L.M., Morrison, C.N., Kaiser, J.T., Rees, D.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Natural Sciences and Engineering Research Council (NSERC, Canada), National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.133 
• R-Value Work: 0.110 
• R-Value Observed: 0.111 

Literature

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 angstrom resolution: comparison with the Azotobacter vinelandii MoFe protein.

Zhang, L.M., Morrison, C.N., Kaiser, J.T., Rees, D.C.

(2015) Acta Crystallogr D Biol Crystallogr 71: 274-282

• PubMed: 25664737 
• DOI: 10.1107/S1399004714025243
• Primary Citation of Related Structures:  
  4WES


• PubMed Abstract: 
  

The X-ray crystal structure of the nitrogenase MoFe protein from Clostridium pasteurianum (Cp1) has been determined at 1.08 Å resolution by multiwavelength anomalous diffraction phasing. Cp1 and the ortholog from Azotobacter vinelandii (Av1) represent two distinct families of nitrogenases, differing primarily by a long insertion in the α-subunit and a deletion in the β-subunit of Cp1 relative to Av1. Comparison of these two MoFe protein structures at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The FeMo cofactors defining the active sites of the MoFe protein are essentially identical between the two proteins. The surrounding environment is also highly conserved, suggesting that this structural arrangement is crucial for nitrogen reduction. The P clusters are likewise similar, although the surrounding protein and solvent environment is less conserved relative to that of the FeMo cofactor. The P cluster and FeMo cofactor in Av1 and Cp1 are connected through a conserved water tunnel surrounded by similar secondary-structure elements. The long α-subunit insertion loop occludes the presumed Fe protein docking surface on Cp1 with few contacts to the remainder of the protein. This makes it plausible that this loop is repositioned to open up the Fe protein docking surface for complex formation.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	534	Clostridium pasteurianum DSM 525 = ATCC 6013	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P00467 (Clostridium pasteurianum) Explore P00467  Go to UniProtKB:  P00467

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	458	Clostridium pasteurianum DSM 525 = ATCC 6013	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P11347 (Clostridium pasteurianum) Explore P11347  Go to UniProtKB:  P11347

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ICS	F [auth A], L [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe7 Mo S9 DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF	H [auth A], M [auth C]	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-DHHOTQGYAO
HCA	E [auth A], K [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C7 H10 O7 XKJVEVRQMLKSMO-SSDOTTSWSA-N
MPD	G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
FE2	I [auth B], J [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.133 
• R-Value Work: 0.110 
• R-Value Observed: 0.111 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.701	α = 90
b = 170.581	β = 91.63
c = 87.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-09-10 
• Released Date: 2015-02-11 
Deposition Author(s): Zhang, L.M., Morrison, C.N., Kaiser, J.T., Rees, D.C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM45162
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--
National Science Foundation (NSF, United States)	United States	DGE-1144469

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Advisory, Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence