4WES

Nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 1.08 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 angstrom resolution: comparison with the Azotobacter vinelandii MoFe protein.

Zhang, L.M.Morrison, C.N.Kaiser, J.T.Rees, D.C.

(2015) Acta Crystallogr.,Sect.D 71: 274-282

  • DOI: 10.1107/S1399004714025243

  • PubMed Abstract: 
  • The X-ray crystal structure of the nitrogenase MoFe protein from Clostridium pasteurianum (Cp1) has been determined at 1.08 Å resolution by multiwavelength anomalous diffraction phasing. Cp1 and the ortholog from Azotobacter vinelandii (Av1) represen ...

    The X-ray crystal structure of the nitrogenase MoFe protein from Clostridium pasteurianum (Cp1) has been determined at 1.08 Å resolution by multiwavelength anomalous diffraction phasing. Cp1 and the ortholog from Azotobacter vinelandii (Av1) represent two distinct families of nitrogenases, differing primarily by a long insertion in the α-subunit and a deletion in the β-subunit of Cp1 relative to Av1. Comparison of these two MoFe protein structures at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The FeMo cofactors defining the active sites of the MoFe protein are essentially identical between the two proteins. The surrounding environment is also highly conserved, suggesting that this structural arrangement is crucial for nitrogen reduction. The P clusters are likewise similar, although the surrounding protein and solvent environment is less conserved relative to that of the FeMo cofactor. The P cluster and FeMo cofactor in Av1 and Cp1 are connected through a conserved water tunnel surrounded by similar secondary-structure elements. The long α-subunit insertion loop occludes the presumed Fe protein docking surface on Cp1 with few contacts to the remainder of the protein. This makes it plausible that this loop is repositioned to open up the Fe protein docking surface for complex formation.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase molybdenum-iron protein alpha chain
A, C
534Clostridium pasteurianumMutation(s): 0 
Gene 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 pasteurianumMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
Find proteins for P11347 (Clostridium pasteurianum)
Go to UniProtKB:  P11347
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download SDF File 
Download CCD File 
B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
ICS
Query on ICS

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Download CCD File 
A, C
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CLF
Query on CLF

Download SDF File 
Download CCD File 
A, C
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
HCA
Query on HCA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.110 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.701α = 90.00
b = 170.581β = 91.63
c = 87.540γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM45162
Natural Sciences and Engineering Research Council (Canada)Canada--
National Science Foundation (United States)United StatesDGE-1144469

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Advisory, Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy