1L5H

FeMo-cofactor Deficient Nitrogenase MoFe Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a cofactor-deficient nitrogenase MoFe protein.

Schmid, B.Ribbe, M.W.Einsle, O.Yoshida, M.Thomas, L.M.Dean, D.R.Rees, D.C.Burgess, B.K.

(2002) Science 296: 352-356

  • DOI: 10.1126/science.1070010
  • Primary Citation of Related Structures:  
    1L5H

  • PubMed Abstract: 
  • One of the most complex biosynthetic processes in metallobiochemistry is the assembly of nitrogenase, the key enzyme in biological nitrogen fixation. We describe here the crystal structure of an iron-molybdenum cofactor-deficient form of the nitrogenase MoFe protein, into which the cofactor is inserted in the final step of MoFe protein assembly ...

    One of the most complex biosynthetic processes in metallobiochemistry is the assembly of nitrogenase, the key enzyme in biological nitrogen fixation. We describe here the crystal structure of an iron-molybdenum cofactor-deficient form of the nitrogenase MoFe protein, into which the cofactor is inserted in the final step of MoFe protein assembly. The MoFe protein folds as a heterotetramer containing two copies each of the homologous alpha and beta subunits. In this structure, one of the three alpha subunit domains exhibits a substantially changed conformation, whereas the rest of the protein remains essentially unchanged. A predominantly positively charged funnel is revealed; this funnel is of sufficient size to accommodate insertion of the negatively charged cofactor.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, Mail Code 147-75CH, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nitrogenase molybdenum-iron protein alpha chainA491Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifD
EC: 1.18.6.1
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nitrogenase molybdenum-iron protein beta chainB522Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLF
Query on CLF

Download Ideal Coordinates CCD File 
D [auth B]FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.452α = 90
b = 191.922β = 90
c = 102.339γ = 90
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-17
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance