1H1L

NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, NIFV MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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. Moreove ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAIN
A, C
481Klebsiella pneumoniaeGene Names: nifD
EC: 1.18.6.1
Find proteins for P00466 (Klebsiella pneumoniae)
Go to UniProtKB:  P00466
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NITROGENASE MOLYBDENUM IRON PROTEIN BETA CHAIN
B, D
519Klebsiella pneumoniaeGene Names: nifK
EC: 1.18.6.1
Find proteins for P09772 (Klebsiella pneumoniae)
Go to UniProtKB:  P09772
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

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A, C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
CFM
Query on CFM

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Download CCD File 
A, C
FE-MO-S CLUSTER
Fe7 Mo S9
UZRXIPMKRKMLQF-VGXFRCDIAP
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CLF
Query on CLF

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Download CCD File 
B, D
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 204.060α = 90.00
b = 75.060β = 123.95
c = 164.260γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance