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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/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). 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAIN
A, C
481Klebsiella pneumoniaeMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P00466 (Klebsiella pneumoniae)
Explore P00466 
Go to UniProtKB:  P00466
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00466
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NITROGENASE MOLYBDENUM IRON PROTEIN BETA CHAIN
B, D
519Klebsiella pneumoniaeMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P09772 (Klebsiella pneumoniae)
Explore P09772 
Go to UniProtKB:  P09772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09772
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / 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-UHFFFAOYSA-N
CLF
Query on CLF

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

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

Download Ideal Coordinates CCD File 
J [auth B],
O [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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
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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description