1DXR

Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant (terbutryn complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of the drastically increased initial electron transfer rate in the reaction center from a Rhodopseudomonas viridis mutant described at 2.00-A resolution.

Lancaster, C.R.Bibikova, M.V.Sabatino, P.Oesterhelt, D.Michel, H.

(2000) J Biol Chem 275: 39364-39368

  • DOI: 10.1074/jbc.M008225200
  • Primary Citation of Related Structures:  
    1DXR

  • PubMed Abstract: 
  • It has previously been shown that replacement of the residue His L168 with Phe (HL168F) in the Rhodopseudomonas viridis reaction center (RC) leads to an unprecedented drastic acceleration of the initial electron transfer rate. Here we describe the determination of the x-ray crystal structure at 2 ...

    It has previously been shown that replacement of the residue His L168 with Phe (HL168F) in the Rhodopseudomonas viridis reaction center (RC) leads to an unprecedented drastic acceleration of the initial electron transfer rate. Here we describe the determination of the x-ray crystal structure at 2.00-A resolution of the HL168F RC. The electron density maps confirm that a hydrogen bond from the protein to the special pair is removed by this mutation. Compared with the wild-type RC, the acceptor of this hydrogen bond, the ring I acetyl group of the "special pair" bacteriochlorophyll, D(L), is rotated, and its acetyl oxygen is found 1.1 A closer to the bacteriochlorophyll-Mg(2+) of the other special pair bacteriochlorophyll, D(M). The rotation of this acetyl group and the increased interaction between the D(L) ring I acetyl oxygen and the D(M)-Mg(2+) provide the structural basis for the previously observed 80-mV decrease in the D(+)/D redox potential and the drastically increased rate of initial electron transfer to the accessory bacteriochlorophyll, B(A). The high quality of the electron density maps also allowed a reliable discussion of the mode of binding of the triazine herbicide terbutryn at the binding site of the secondary quinone, Q(B).


    Related Citations: 
    • Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid
      Lancaster, C.R., Michel, H.
      (1999) J Mol Biol 286: 883
    • Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications
      Lancaster, C.R.D.
      (1998) Biochim Biophys Acta 1365: 143
    • The Coupling of Light-Induced Electron Transfer and Proton Uptake as Derived from Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb
      Lancaster, C.R., Michel, H.
      (1997) Structure 5: 1339
    • Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Deisenhofer, J., Epp, O., Sinning, I., Michel, H.
      (1995) J Mol Biol 246: 429
    • The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis
      Deisenhofer, J., Michel, H.
      (1989) Science 245: 1463
    • Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution
      Deisenhofer, J., Epp, O., Miki, K., Huber, R., Michel, H.
      (1985) Nature 318: 618
    • X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis
      Deisenhofer, J., Epp, O., Miki, K., Huber, R., Michel, H.
      (1984) J Mol Biol 180: 385
    • Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Michel, H.
      (1982) J Mol Biol 158: 567

    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Abteilung Molekulare Membranbiologie, Heinrich-Hoffmann Str. 7, D-60528 Frankfurt am Main, Germany. Roy.Lancaster@mpibp-frankfurt.mpg.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNITA [auth C]336Blastochloris viridisMutation(s): 0 
Gene Names: pufCcytCBVIRIDIS_00500
Membrane Entity: Yes 
UniProt
Find proteins for P07173 (Blastochloris viridis)
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Go to UniProtKB:  P07173
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER H SUBUNITB [auth H]258Blastochloris viridisMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P06008 (Blastochloris viridis)
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Go to UniProtKB:  P06008
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER L SUBUNITC [auth L]273Blastochloris viridisMutation(s): 1 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER M SUBUNITD [auth M]323Blastochloris viridisMutation(s): 0 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCB (Subject of Investigation/LOI)
Query on BCB

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L, M [auth L], S [auth M], T [auth M]BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
BPB (Subject of Investigation/LOI)
Query on BPB

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N [auth L], U [auth M]BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
MQ9 (Subject of Investigation/LOI)
Query on MQ9

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P [auth L]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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E [auth C], F [auth C], G [auth C], H [auth C]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
NS5 (Subject of Investigation/LOI)
Query on NS5

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V [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
MST (Subject of Investigation/LOI)
Query on MST

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Q [auth L]2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE
C10 H19 N5 S
IROINLKCQGIITA-UHFFFAOYSA-N
 Ligand Interaction
LDA (Subject of Investigation/LOI)
Query on LDA

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I [auth H], J [auth H], R [auth L], W [auth M], X [auth M], Y [auth M]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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AA [auth M], BA [auth M], K [auth H], Z [auth M]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
O [auth L]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
B [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.5α = 90
b = 223.5β = 90
c = 113.6γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-12
    Type: Initial release
  • Version 1.1: 2011-07-27
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2012-02-08
    Changes: Other
  • Version 1.3: 2014-09-03
    Changes: Database references, Structure summary
  • Version 1.4: 2018-11-14
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary