1M1N | pdb_00001m1n

Nitrogenase MoFe protein from Azotobacter vinelandii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.149 (Depositor) 
  • R-Value Work: 
    0.123 (Depositor) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1M1N

This is version 1.3 of the entry. See complete history

Literature

Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor.

Einsle, O.Tezcan, F.A.Andrade, S.L.Schmid, B.Yoshida, M.Howard, J.B.Rees, D.C.

(2002) Science 297: 1696-1700

  • DOI: https://doi.org/10.1126/science.1073877
  • Primary Citation Related Structures: 
    1M1N

  • PubMed Abstract: 

    A high-resolution crystallographic analysis of the nitrogenase MoFe-protein reveals a previously unrecognized ligand coordinated to six iron atoms in the center of the catalytically essential FeMo-cofactor. The electron density for this ligand is masked in structures with resolutions lower than 1.55 angstroms, owing to Fourier series termination ripples from the surrounding iron and sulfur atoms in the cofactor. The central atom completes an approximate tetrahedral coordination for the six iron atoms, instead of the trigonal coordination proposed on the basis of lower resolution structures. The crystallographic refinement at 1.16 angstrom resolution is consistent with this newly detected component being a light element, most plausibly nitrogen. The presence of a nitrogen atom in the cofactor would have important implications for the mechanism of dinitrogen reduction by nitrogenase.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 147-75CH, Pasadena, CA 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 465.37 kDa 
  • Atom Count: 37,384 
  • Modeled Residue Count: 3,996 
  • Deposited Residue Count: 4,052 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C, E, G
491Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07328
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D, F, H
522Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07329
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CFN

Query on CFN



Download:Ideal Coordinates CCD File
J [auth A],
N [auth C],
R [auth E],
V [auth G]
FE(7)-MO-S(9)-N CLUSTER
Fe7 Mo N S9
OSSJGSCTDHHOOW-UHFFFAOYSA-N
CLF

Query on CLF



Download:Ideal Coordinates CCD File
L [auth B],
P [auth D],
T [auth F],
X [auth H]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA

Query on HCA



Download:Ideal Coordinates CCD File
I [auth A],
M [auth C],
Q [auth E],
U [auth G]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth B],
O [auth D],
S [auth F],
W [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.149 (Depositor) 
  • R-Value Work:  0.123 (Depositor) 
  • R-Value Observed: 0.123 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.31α = 90
b = 131.63β = 108.37
c = 159.159γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description