2UXJ

X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 10 in the neutral state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ph Modulates the Quinone Position in the Photosynthetic Reaction Center from Rhodobacter Sphaeroides in the Neutral and Charge Separated States.

Koepke, J.Krammer, E.M.Klingen, A.R.Sebban, P.Ullmann, G.M.Fritzsch, G.

(2007) J.Mol.Biol. 371: 396

  • DOI: 10.1016/j.jmb.2007.04.082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolut ...

    The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolution of 1.87 A, which is the best ever reported for the bacterial reaction center protein. Our crystallographic data confirm the existence of two different binding positions of the secondary quinone (QB). We observe a new orientation of QB in its distal position, which shows no ring-flip compared to the orientation in the proximal position. Datasets collected for the different pH values show a pH-dependence of the population of the proximal position. The new orientation of QB in the distal position and the pH-dependence could be confirmed by continuum electrostatics calculations. Our calculations are in agreement with the experimentally observed proton uptake upon charge separation. The high resolution of our crystallographic data allows us to identify new water molecules and external residues being involved in two previously described hydrogen bond proton channels. These extended proton-transfer pathways, ending at either of the two oxo-groups of QB in its proximal position, provide additional evidence that ring-flipping is not required for complete protonation of QB upon reduction.


    Organizational Affiliation

    Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue Strasse 3, D-60438 Frankfurt/Main, Germany. Juergen.Koepke@mpibp-frankfurt.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAIN
H
260Rhodobacter sphaeroidesGene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN L CHAIN
L
281Rhodobacter sphaeroidesGene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN M CHAIN
M
307Rhodobacter sphaeroidesGene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
U10
Query on U10

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M
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
CDL
Query on CDL

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M
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
GOL
Query on GOL

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H, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCL
Query on BCL

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L, M
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
LDA
Query on LDA

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L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

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L
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
BPH
Query on BPH

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L, M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
UQ2
Query on UQ2

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L
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
SPO
Query on SPO

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M
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 139.376α = 90.00
b = 139.376β = 90.00
c = 235.041γ = 90.00
Software Package:
Software NamePurpose
HKLdata reduction
CNSphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance