1AIJ

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer.

Stowell, M.H.McPhillips, T.M.Rees, D.C.Soltis, S.M.Abresch, E.Feher, G.

(1997) Science 276: 812-816

  • DOI: 10.1126/science.276.5313.812
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • High resolution x-ray diffraction data from crystals of the Rhodobacter sphaeroides photosynthetic reaction center (RC) have been collected at cryogenic temperature in the dark and under illumination, and the structures were refined at 2.2 and 2.6 an ...

    High resolution x-ray diffraction data from crystals of the Rhodobacter sphaeroides photosynthetic reaction center (RC) have been collected at cryogenic temperature in the dark and under illumination, and the structures were refined at 2.2 and 2.6 angstrom resolution, respectively. In the charge-separated D+QAQB- state (where D is the primary electron donor (a bacteriochlorophyll dimer), and QA and QB are the primary and secondary quinone acceptors, respectively), QB- is located approximately 5 angstroms from the QB position in the charge-neutral (DQAQB) state, and has undergone a 180 degrees propeller twist around the isoprene chain. A model based on the difference between the two structures is proposed to explain the observed kinetics of electron transfer from QA-QB to QAQB- and the relative binding affinities of the different ubiquinone species in the QB pocket. In addition, several water channels (putative proton pathways) leading from the QB pocket to the surface of the RC were delineated, one of which leads directly to the membrane surface.


    Related Citations: 
    • Structure and Function of Bacterial Photosynthetic Reaction Centres
      Feher, G., Allen, J.P., Okamura, M.Y., Rees, D.C.
      (1989) Nature 339: 111
    • The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins
      Rees, D.C., Komiya, H., Yeates, T.O., Allen, J.P., Feher, G.
      (1989) Annu Rev Biochem 58: 607
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26 and 2.4.1: Protein-Cofactor (Bacteriochlorophyll, Bacteriopheophytin, and Carotenoid) Interactions
      Yeates, T.O., Komiya, H., Chirino, A., Rees, D.C., Allen, J.P., Feher, G.
      (1988) Proc Natl Acad Sci U S A 85: 7993
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26 and 2.4.1: Symmetry Relations and Sequence Comparisons between Different Species
      Komiya, H., Yeates, T.O., Rees, D.C., Allen, J.P., Feher, G.
      (1988) Proc Natl Acad Sci U S A 85: 9012
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Protein-Cofactor (Quinones and Fe2+) Interactions
      Allen, J.P., Feher, G., Yeates, T.O., Komiya, H., Rees, D.C.
      (1988) Proc Natl Acad Sci U S A 85: 8487
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Protein Subunits
      Allen, J.P., Feher, G., Yeates, T.O., Komiya, H., Rees, D.C.
      (1987) Proc Natl Acad Sci U S A 84: 6162
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Cofactors
      Allen, J.P., Feher, G., Yeates, T.O., Komiya, H., Rees, D.C.
      (1987) Proc Natl Acad Sci U S A 84: 5730
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Membrane-Protein Interactions
      Yeates, T.O., Komiya, H., Rees, D.C., Allen, J.P., Feher, G.
      (1987) Proc Natl Acad Sci U S A 84: 6438
    • Structural Homology of Reaction Centers from Rhodopseudomonas Sphaeroides and Rhodopseudomonas Viridis as Determined by X-Ray Diffraction
      Allen, J.P., Feher, G., Yeates, T.O., Rees, D.C., Deisenhofer, J., Michel, H., Huber, R.
      (1986) Proc Natl Acad Sci U S A 83: 8589
    • Crystallization of Reaction Center from Rhodopseudomonas Sphaeroides: Preliminary Characterization
      Allen, J.P., Feher, G.
      (1984) Proc Natl Acad Sci U S A 81: 4795

    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, 147-75CH, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)L, R281Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)M, S307Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)H, T260Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

Download CCD File 
L, M, R, S
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH
Query on BPH

Download CCD File 
L, R, S
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10
Query on U10

Download CCD File 
L, M, R, S
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
LDA
Query on LDA

Download CCD File 
M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
M, S
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.08α = 90
b = 140.08β = 90
c = 271.63γ = 90
Software Package:
Software NamePurpose
MERLOTphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Database references, Derived calculations