4TKV

CO-bound Nitrogenase MoFe-protein from A. vinelandii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase.

Spatzal, T.Perez, K.A.Einsle, O.Howard, J.B.Rees, D.C.

(2014) Science 345: 1620-1623

  • DOI: 10.1126/science.1256679
  • Primary Citation of Related Structures:  
    4TKU, 4TKV

  • PubMed Abstract: 
  • The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1 ...

    The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The μ2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.


    Organizational Affiliation

    Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, MailCode 114-96, California Institute of Technology, Pasadena, CA 91125, USA. spatzal@caltech.edu dcrees@caltech.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chainA, C492Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifD
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chainB, D523Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifK
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ICE
Query on ICE

Download Ideal Coordinates CCD File 
F [auth A],
J [auth A],
S [auth C],
W [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S8
BJBPMDQXUSSDMI-UHFFFAOYSA-N
 Ligand Interaction
CLF
Query on CLF

Download Ideal Coordinates CCD File 
K [auth A],
X [auth C]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
HCA
Query on HCA

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

Download Ideal Coordinates CCD File 
AA [auth D],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
AA [auth D],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
T [auth C],
Y [auth D],
Z [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
BA [auth D],
H [auth A],
I [auth A],
O [auth B],
U [auth C],
BA [auth D],
H [auth A],
I [auth A],
O [auth B],
U [auth C],
V [auth C]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.172α = 90
b = 130.623β = 110.65
c = 106.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 2.0: 2019-08-21
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy