7TPV

Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (5mM KSeCN Soaked)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Selenocyanate derived Se-incorporation into the Nitrogenase Fe protein cluster.

Buscagan, T.M.Kaiser, J.T.Rees, D.C.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.79311
  • Primary Citation of Related Structures:  
    7T4H, 7TNE, 7TPN, 7TPO, 7TPV, 7TPW, 7TPX, 7TPY, 7TPZ, 7TQ0, 7TQ9, 7TQC, 7TQE, 7TQF, 7TQH, 7TQI, 7TQJ, 7TQK

  • PubMed Abstract: 

    The nitrogenase Fe protein mediates ATP-dependent electron transfer to the nitrogenase MoFe protein during nitrogen fixation, in addition to catalyzing MoFe protein-independent substrate (CO 2 ) reduction and facilitating MoFe protein metallocluster biosynthesis. The precise role(s) of the Fe protein Fe 4 S 4 cluster in some of these processes remains ill-defined. Herein, we report crystallographic data demonstrating ATP-dependent chalcogenide exchange at the Fe 4 S 4 cluster of the nitrogenase Fe protein when potassium selenocyanate is used as the selenium source, an unexpected result as the Fe protein cluster is not traditionally perceived as a site of substrate binding within nitrogenase. The observed chalcogenide exchange illustrates that this Fe 4 S 4 cluster is capable of core substitution reactions under certain conditions, adding to the Fe protein's repertoire of unique properties.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein 1290Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
Explore P00459 
Go to UniProtKB:  P00459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00459
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.363α = 90
b = 73.691β = 90
c = 74.17γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description