1H1L

NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, NIFV MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic Analysis of the Mofe Protein of Nitrogenase from a Nifv Mutant of Klebsiella Pneumoniae Identifies Citrate as a Ligand to the Molybdenum of Iron Molybdenum Cofactor (Femoco).

Mayer, S.M.Gormal, C.A.Smith, B.E.Lawson, D.M.

(2002) J Biol Chem 277: 35263

  • DOI: 10.1074/jbc.M205888200
  • Primary Citation of Related Structures:  
    1H1L

  • PubMed Abstract: 
  • The x-ray crystal structure of NifV(-) Klebsiella pneumoniae nitrogenase MoFe protein (NifV(-) Kp1) has been determined and refined to a resolution of 1.9 A. This is the first structure for a nitrogenase MoFe protein with an altered cofactor. Moreover, it is the first direct evidence that the organic acid citrate is not just present, but replaces homocitrate as a ligand to the molybdenum atom of the iron molybdenum cofactor (FeMoco) ...

    The x-ray crystal structure of NifV(-) Klebsiella pneumoniae nitrogenase MoFe protein (NifV(-) Kp1) has been determined and refined to a resolution of 1.9 A. This is the first structure for a nitrogenase MoFe protein with an altered cofactor. Moreover, it is the first direct evidence that the organic acid citrate is not just present, but replaces homocitrate as a ligand to the molybdenum atom of the iron molybdenum cofactor (FeMoco). Subsequent refinement of the structure revealed that the citrate was present at reduced occupancy.


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAINA, C481Klebsiella pneumoniaeMutation(s): 0 
Gene Names: nifD
EC: 1.18.6.1
UniProt
Find proteins for P00466 (Klebsiella pneumoniae)
Explore P00466 
Go to UniProtKB:  P00466
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 CHAINB, D519Klebsiella pneumoniaeMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
UniProt
Find proteins for P09772 (Klebsiella pneumoniae)
Explore P09772 
Go to UniProtKB:  P09772
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFM
Query on CFM

Download Ideal Coordinates CCD File 
F [auth A], N [auth C]FE-MO-S CLUSTER
Fe7 Mo S9
UZRXIPMKRKMLQF-VGXFRCDIAP
 Ligand Interaction
CLF
Query on CLF

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

Download Ideal Coordinates CCD File 
E [auth A], M [auth C]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth B], O [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], K [auth B], L [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.06α = 90
b = 75.06β = 123.95
c = 164.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-24
    Changes: Data collection, Experimental preparation, Other