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X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure of the nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 3.0-A resolution.

Kim, J.Woo, D.Rees, D.C.

(1993) Biochemistry 32: 7104-7115


  • PubMed Abstract: 
  • The crystal structure of the nitrogenase molybdenum-iron (MoFe) protein from Clostridium pasteurianum (Cp1) has been determined at 3.0-A resolution by a combination of isomorphous replacement, molecular replacement, and noncrystallographic symmetry a ...

    The crystal structure of the nitrogenase molybdenum-iron (MoFe) protein from Clostridium pasteurianum (Cp1) has been determined at 3.0-A resolution by a combination of isomorphous replacement, molecular replacement, and noncrystallographic symmetry averaging. The structure of Cp1, including the two types of metal centers associated with the protein (the FeMo-cofactor and the P-cluster pair), is similar to that previously described for the MoFe-protein from Azotobacter vinelandii (Av1). Unique features of the Cp1 structure arise from the presence of an approximately 50-residue insertion in the alpha subunit and an approximately 50-residue deletion in the beta subunit. As a consequence, the FeMo-cofactor is more buried in Cp1 than in Av1, since the insertion is located on the surface above the FeMo-cofactor. The location of this insertion near the putative nitrogenase iron protein binding site provides a structural basis for the observation that the nitrogenase proteins from C. pasteurianum have low activity with complementary nitrogenase proteins isolated from other organisms. Mechanistic implications of the Cp1 structure for substrate entry/product release, substrate binding to the FeMo-cofactor, and electron- and proton-transfer reactions of nitrogenase are discussed.


    Related Citations: 
    • Crystallographic Structure and Functional Implications of the Nitrogenase Molybdenum-Iron Protein from Azotobacter Vinelandii
      Kim, J.,Rees, D.C.
      (1992) Nature 360: 553
    • Structural Models for the Metal Centers in the Nitrogenase Molybdenum-Iron Protein
      Kim, J.,Rees, D.C.
      (1992) Science 257: 1677


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROGENASE MOLYBDENUM IRON PROTEIN (ALPHA CHAIN)
A, C
533Clostridium pasteurianumGene Names: nifD
EC: 1.18.6.1
Find proteins for P00467 (Clostridium pasteurianum)
Go to UniProtKB:  P00467
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NITROGENASE MOLYBDENUM IRON PROTEIN (BETA CHAIN)
B, D
458Clostridium pasteurianumGene Names: nifK
EC: 1.18.6.1
Find proteins for P11347 (Clostridium pasteurianum)
Go to UniProtKB:  P11347
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFM
Query on CFM

Download SDF File 
Download CCD File 
B, D
FE-MO-S CLUSTER
Fe7 Mo S9
UZRXIPMKRKMLQF-VGXFRCDIAP
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CLP
Query on CLP

Download SDF File 
Download CCD File 
B, D
FE-S CLUSTER
Fe8 S8
MJXAKWFPOPRKKV-WNHSYQNGAD
 Ligand Interaction
HCA
Query on HCA

Download SDF File 
Download CCD File 
B, D
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.960α = 90.00
b = 151.300β = 110.40
c = 121.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance