1FND

REFINED CRYSTAL STRUCTURE OF SPINACH FERREDOXIN REDUCTASE AT 1.7 ANGSTROMS RESOLUTION: OXIDIZED, REDUCED, AND 2'-PHOSPHO-5'-AMP BOUND STATES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states.

Bruns, C.M.Karplus, P.A.

(1995) J Mol Biol 247: 125-145

  • DOI: 10.1006/jmbi.1994.0127
  • Primary Citation of Related Structures:  
    1FND, 1FNC, 1FNB

  • PubMed Abstract: 
  • The crystal structure of spinach ferredoxin-NADP(+)-oxidoreductase (FNR), determined by multiple isomorphous replacement at 2.6 A resolution, has been refined at 1.7 A resolution to an R-factor of 17.9%. The structure of FNR bound to the competitive inhi ...

    The crystal structure of spinach ferredoxin-NADP(+)-oxidoreductase (FNR), determined by multiple isomorphous replacement at 2.6 A resolution, has been refined at 1.7 A resolution to an R-factor of 17.9%. The structure of FNR bound to the competitive inhibitor 2'-phospho-5'-AMP (P-AMP) has also been refined at 1.7 A to an R-factor of 17.4% and dithionite-reduced/P-AMP-bound FNR has been refined at 2.0 A to an R-factor of 14.9%. The P-AMP-bound structure was used to construct a model for the binding of NADP+. Over 200 solvation sites were included in each structure, and many of the best defined solvation sites stabilize buried turns. A bulk solvent correction obviated the need for a low-resolution data cutoff. An acidic side-chain likely to be responsible for the low pH requirement for crystallization has been identified. Three large networks of the hydrophobic side-chains help define the FNR structure. One of these contains a large cavity far from the active site, which coincides with the lone site of sequence heterogeneity in FNR, and may provide a site for membrane attachment. The reduced structure shows that Ser96 moves toward atom N-5 of FAD and a water molecule moves toward atom N-1 of FAD, while the flavin moiety remains planar. Possible sources of a proton that must be picked up upon reduction are discussed.


    Related Citations: 
    • Atomic Structure of Ferredoxin-Nadp+ Reductase: Prototype for a Structurally Novel Flavoenzyme Family
      Karplus, P.A., Daniels, M.J., Herriott, J.R.
      (1991) Science 251: 60

    Organizational Affiliation

    Section of Biochemistry Molecular, and Cell Biology, Cornell University, Ithaca NY 14853.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERREDOXIN-NADP+ REDUCTASE A314Spinacia oleraceaMutation(s): 0 
Gene Names: PETH
EC: 1.18.1.2
Find proteins for P00455 (Spinacia oleracea)
Explore P00455 
Go to UniProtKB:  P00455
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
A2P
Query on A2P

Download Ideal Coordinates CCD File 
A
ADENOSINE-2'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
AEOBEOJCBAYXBA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.7α = 90
b = 57.7β = 100
c = 68.1γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance