Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.57 kDa 
• Atom Count: 3510 
• Residue Count: 524 
• Unique protein chains: 1

7JMB

Crystal structure of Nitrogenase iron-molybdenum cofactor biosynthesis enzyme NifB from Methanothermobacter thermautotrophicus with three Fe4S4 clusters

• DOI: 10.2210/pdb7JMB/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-31 Released: 2020-10-28 
• Deposition Author(s): Kang, W., Rettberg, L., Ribbe, M.W., Hu, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.314 
• R-Value Work: 0.262 
• R-Value Observed: 0.268 

Literature

X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly.

Kang, W., Rettberg, L.A., Stiebritz, M.T., Jasniewski, A.J., Tanifuji, K., Lee, C.C., Ribbe, M.W., Hu, Y.

(2020) Angew Chem Int Ed Engl 

• PubMed: 33035363 
• DOI: 10.1002/anie.202011367
• Primary Citation of Related Structures:  
  7JMB, 7JMA


• PubMed Abstract: 
  

NifB is an essential radical SAM enzyme required for the assembly of an 8Fe core of the nitrogenase cofactor. Herein, we report the X-ray crystal structures of Methanobacterium thermoautotrophicum NifB without (apo MtNifB) and with (holo MtNifB) a full complement of three [Fe ₄ S ₄ ] clusters. Both apo and holo MtNifB contain a partial TIM barrel core, but unlike apo MtNifB, holo MtNifB is fully assembled and competent in cofactor biosynthesis. The radical SAM (RS)-cluster is coordinated by three Cys, and the adjacent K1- and K2-clusters, representing the precursor to an 8Fe cofactor core, are each coordinated by one His and two Cys. Prediction of substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of SAM between the RS- and K2-clusters and putative paths for entry of SAM and exit of products of SAM cleavage, thereby providing important mechanistic insights into the radical SAM-dependent carbide insertion concomitant with cofactor core formation.

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Organizational Affiliation: 

Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB	A, B	290	Methanothermobacter thermautotrophicus	Mutation(s): 0
Find proteins for O27899 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27899  Go to UniProtKB:  O27899

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	A, B	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.314 
• R-Value Work: 0.262 
• R-Value Observed: 0.268 
• Space Group: C 1 2 1
• Diffraction Data DOI: 10.18430/m37jmb Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.87	α = 90
b = 77.64	β = 128.85
c = 90.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-07-31 
• Released Date: 2020-10-28 
Deposition Author(s): Kang, W., Rettberg, L., Ribbe, M.W., Hu, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM67626
Department of Energy (DOE, United States)	United States	DE-SC0016510

Revision History 

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references
• Version 1.2: 2021-01-20
  Changes: Database references