1PYH

Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.80 Å
  • R-Value Free: 0.491 
  • R-Value Work: 0.467 
  • R-Value Observed: 0.469 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris.

Roszak, A.W.Howard, T.D.Southall, J.Gardiner, A.T.Law, C.J.Isaacs, N.W.Cogdell, R.J.

(2003) Science 302: 1969-1972

  • DOI: https://doi.org/10.1126/science.1088892
  • Primary Citation of Related Structures:  
    1PYH

  • PubMed Abstract: 

    The crystal structure at 4.8 angstrom resolution of the reaction center-light harvesting 1 (RC-LH1) core complex from Rhodopseudomonas palustris shows the reaction center surrounded by an oval LH1 complex that consists of 15 pairs of transmembrane helical alpha- and beta-apoproteins and their coordinated bacteriochlorophylls. Complete closure of the RC by the LH1 is prevented by a single transmembrane helix, out of register with the array of inner LH1 alpha-apoproteins. This break, located next to the binding site in the reaction center for the secondary electron acceptor ubiquinone (UQB), may provide a portal through which UQB can transfer electrons to cytochrome b/c1.


  • Organizational Affiliation

    Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chain281Rhodopseudomonas palustrisMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chain302Rhodopseudomonas palustrisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chain241Rhodopseudomonas palustrisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850, alpha chain26Rhodopseudomonas palustrisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850, beta chain30Rhodopseudomonas palustrisMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

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AB [auth N]
BB [auth P]
CB [auth P]
DB [auth R]
EB [auth S]
AB [auth N],
BB [auth P],
CB [auth P],
DB [auth R],
EB [auth S],
FB [auth T],
GB [auth U],
HB [auth V],
IA [auth A],
IB [auth W],
JA [auth A],
JB [auth Y],
KB [auth Y],
LB [auth 1],
MA [auth B],
MB [auth 2],
NA [auth B],
NB [auth 3],
OB [auth 3],
PA [auth D],
PB [auth 5],
QA [auth E],
QB [auth 6],
RA [auth F],
RB [auth 7],
SA [auth G],
SB [auth 8],
TA [auth H],
UA [auth I],
VA [auth J],
WA [auth K],
XA [auth L],
YA [auth M],
ZA [auth N]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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KA [auth A],
OA [auth B]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
FE
Query on FE

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LA [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.80 Å
  • R-Value Free: 0.491 
  • R-Value Work: 0.467 
  • R-Value Observed: 0.469 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.037α = 69.32
b = 119.024β = 72.69
c = 130.432γ = 66.52
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description