3U7Q

A. vinelandii nitrogenase MoFe protein at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.1214025

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase molybdenum-iron protein alpha chain
A, C
492Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifD
EC: 1.18.6.1
Find proteins for P07328 (Azotobacter vinelandii)
Go to UniProtKB:  P07328
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
Find proteins for P07329 (Azotobacter vinelandii)
Go to UniProtKB:  P07329
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1CL
Query on 1CL

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Download CCD File 
B, D
FE(8)-S(7) CLUSTER, OXIDIZED
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A, B, C, D
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 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
CLF
Query on CLF

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Download CCD File 
B, D
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 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.128 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.190α = 90.00
b = 130.696β = 110.67
c = 107.224γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Advisory, Refinement description