1QGU

NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, DITHIONITE-REDUCED STATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.156 

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This is version 1.2 of the entry. See complete history. 


Literature

New insights into structure-function relationships in nitrogenase: A 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein.

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

(1999) J Mol Biol 292: 871-891

  • DOI: 10.1006/jmbi.1999.3107
  • Primary Citation of Related Structures:  
    1QGU, 1QH1, 1QH8

  • PubMed Abstract: 

    • The X-ray crystal structure of Klebsiella pneumoniae nitrogenase component 1 (Kp1) has been determined and refined to a resolution of 1.6 A, the highest resolution reported for any nitrogenase structure. Models derived from three 1.6 A resolution X-ray data sets are described; two represent distinct oxidation states, whilst the third appears to be a mixture of both oxidized and reduced states (or perhaps an intermediate state) ...

    The X-ray crystal structure of Klebsiella pneumoniae nitrogenase component 1 (Kp1) has been determined and refined to a resolution of 1.6 A, the highest resolution reported for any nitrogenase structure. Models derived from three 1.6 A resolution X-ray data sets are described; two represent distinct oxidation states, whilst the third appears to be a mixture of both oxidized and reduced states (or perhaps an intermediate state). The structures of the protein and the iron-molybdenum cofactor (FeMoco) appear to be largely unaffected by the redox status, although the movement of Ser beta90 and a surface helix in the beta subunit may be of functional significance. By contrast, the 8Fe-7S P-cluster undergoes discrete conformational changes involving the movement of two iron atoms. Comparisons with known component 1 structures reveal subtle differences in the FeMoco environment, which could account for the lower midpoint potential of this cluster in Kp1. Furthermore, a non-proline- cis peptide bond has been identified in the alpha subunit that may have a functional role. It is within 10 A of the FeMoco and may have been overlooked in other component 1 models. Finally, metal-metal and metal-sulphur distances within the metal clusters agree well with values derived from EXAFS studies, although they are generally longer than the values reported for the closely related protein from Azotobacter vinelandii. A number of bonds between the clusters and their ligands are distinctly longer than the EXAFS values, in particular, those involving the molybdenum atom of the FeMoco.

    Organizational Affiliation: 

    John Innes Centre, Nitrogen Fixation Laboratory, Norwich, NR4 7UH, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)A, C478Klebsiella pneumoniaeMutation(s): 0 
Gene Names: nifD
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)B, 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09772
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFM
Query on CFM
Download Ideal Coordinates CCD File 
G [auth A],
X [auth C]		FE-MO-S CLUSTER
Fe7 Mo S9
UZRXIPMKRKMLQF-VGXFRCDIAP		 Ligand Interaction
CLF
Query on CLF
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H [auth A],
Y [auth C]		FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO		 Ligand Interaction
HCA
Query on HCA
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F [auth A],
W [auth C]		3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N		 Ligand Interaction
EDO
Query on EDO
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DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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AA [auth D],
N [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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BA [auth D],
CA [auth D],
E [auth A],
O [auth B],
P [auth B],
BA [auth D],
CA [auth D],
E [auth A],
O [auth B],
P [auth B],
Q [auth B],
V [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.03α = 90
b = 75.3β = 122.61
c = 163.01γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-01
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance