1KBY

Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of the heterodimer reaction center from Rhodobacter sphaeroides at 2.55 a resolution.

Camara-Artigas, A.Magee, C.Goetsch, A.Allen, J.P.

(2002) Photosynth.Res. 74: 87-93

  • DOI: 10.1023/A:1020882402389

  • PubMed Abstract: 
  • Crystals have been obtained of reaction centers of the heterodimer mutant that has significantly different properties than wild type due to the primary donor being formed from both a bacteriochlorophyll and bacteriopheophytin rather than two bacterio ...

    Crystals have been obtained of reaction centers of the heterodimer mutant that has significantly different properties than wild type due to the primary donor being formed from both a bacteriochlorophyll and bacteriopheophytin rather than two bacteriochlorophylls as found for wild type. The crystals belong to the trigonal space group P3(1)21 and the structure has been refined to a resolution limit of 2.55 A with an R factor of 19.0%. The electron density maps confirm that a primary donor does indeed contain a bacteriopheophytin due to the His to Leu substitution at M202 that coordinates the corresponding bacteriochlorophyll in wild-type. Other structural changes compared to wild type are relatively minor with the relative orientation and positioning of the two tetrapyrroles forming the primary donor being unchanged within the error. Compared to wild type, the only significant alterations are small shifts of residues M196 to M206, a rotation of the side chain of Ile M206, and the loss of a bound water molecule that in wild-type is hydrogen-bonded to both His M202 and the bacteriochlorophyll monomer on the active branch. Since hydrogen-bonding interactions strongly influence the energies of tetrapyrroles, the loss of the water molecule should result in changes in the energies of the bacteriochlorophyll monomer that contributes to the observed functional differences with wild-type.


    Related Citations: 
    • Effects of Hydrogen Bonding to a Bacteriochklorophyll-bacteriopheophytin Dimer in Reaction Centers from Rhodobacter Sphaeroides
      Allen, J.P.,Artz, K.,Lin, X.,Williams, J.C.,Ivancich, A.,Albouy, D.,Mattioli, T.A.,Fetsch, A.,Kuhn, M.,Lubitz, W.
      (1996) Biochemistry 35: 6612


    Organizational Affiliation

    Center for the Study of Early Events in Photosynthesis and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-1604, USA, jallen@asu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER PROTEIN L CHAIN
L
281Rhodobacter sphaeroidesGene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER PROTEIN M CHAIN
M
307Rhodobacter sphaeroidesMutations: H202L
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER PROTEIN H CHAIN
H
260Rhodobacter sphaeroidesGene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
CL
Query on CL

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M
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BCL
Query on BCL

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L
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
FE
Query on FE

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

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L, M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-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: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.310α = 90.00
b = 142.310β = 90.00
c = 187.590γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation