3EOJ | pdb_00003eoj

Fmo protein from Prosthecochloris Aestuarii 2K AT 1.3A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.161 (Depositor), 0.149 (DCC) 
  • R-Value Work: 
    0.135 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria.

Tronrud, D.E.Wen, J.Gay, L.Blankenship, R.E.

(2009) Photosynth Res 100: 79-87

  • DOI: https://doi.org/10.1007/s11120-009-9430-6
  • Primary Citation Related Structures: 
    3ENI, 3EOJ

  • PubMed Abstract: 

    The absorbance spectrum of the Fenna-Matthews-Olson protein--a component of the antenna system of Green Sulfur Bacteria--is always one of two types, depending on the species of the source organism. The FMO from Prosthecochloris aestuarii 2K has a spectrum of type 1 while that from Chlorobaculum tepidum is of type 2. The previously reported crystal structures for these two proteins did not disclose any rationale that would explain their spectral differences. We have collected a 1.3 A X-ray diffraction dataset of the FMO from Prosthecochloris aestuarii 2K, which has allowed us to identify an additional Bacteriochlorophyll-a molecule with chemical attachments to both sides of the central magnesium atom. A new analysis of the previously published X-ray data for the Chlorobaculum tepidum FMO shows the presence of a Bacteriochlorophyll-a molecule in an equivalent location but with a chemical attachment from only one side. This difference in binding is shown to be predictive of the spectral type of the FMO.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA. det101@daletronrud.com

Macromolecule Content 

  • Total Structure Weight: 48.55 kDa 
  • Atom Count: 4,115 
  • Modeled Residue Count: 359 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacteriochlorophyll a protein366Prosthecochloris aestuariiMutation(s): 0 
UniProt
Find proteins for P11741 (Prosthecochloris aestuarii)
Explore P11741 
Go to UniProtKB:  P11741
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11741
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on BCL



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
Y [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4

Query on NH4



Download:Ideal Coordinates CCD File
Z [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.161 (Depositor), 0.149 (DCC) 
  • R-Value Work:  0.135 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.242α = 90
b = 111.242β = 90
c = 98.198γ = 120
Software Package:
Software NamePurpose
ARP/wARPmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-12-18
    Changes: Other
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description