3U7Q

A. vinelandii nitrogenase MoFe protein at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evidence for interstitial carbon in nitrogenase FeMo cofactor.

Spatzal, T.Aksoyoglu, M.Zhang, L.Andrade, S.L.Schleicher, E.Weber, S.Rees, D.C.Einsle, O.

(2011) Science 334: 940-940

  • DOI: https://doi.org/10.1126/science.1214025
  • Primary Citation of Related Structures:  
    3U7Q

  • PubMed Abstract: 

    The identity of the interstitial light atom in the center of the FeMo cofactor of nitrogenase has been enigmatic since its discovery. Atomic-resolution x-ray diffraction data and an electron spin echo envelope modulation (ESEEM) analysis now provide direct evidence that the ligand is a carbon species.


  • Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C
492Azotobacter 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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter 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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS
Query on ICS

Download Ideal Coordinates CCD File 
F [auth A],
Q [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
1CL
Query on 1CL

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J [auth B],
T [auth D]
FE(8)-S(7) CLUSTER, OXIDIZED
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
CLF
Query on CLF

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

Download Ideal Coordinates CCD File 
E [auth A],
P [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
IMD
Query on IMD

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G [auth A]
H [auth A]
M [auth B]
N [auth B]
R [auth C]
G [auth A],
H [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
U [auth D],
W [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CA
Query on CA

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I [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
O [auth B],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.19α = 90
b = 130.696β = 110.67
c = 107.224γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.2: 2023-09-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description