1YF6 | pdb_00001yf6

Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.216 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Quinone (Q(B)) Reduction by B-Branch Electron Transfer in Mutant Bacterial Reaction Centers from Rhodobacter sphaeroides: Quantum Efficiency and X-ray Structure.

Paddock, M.L.Chang, C.Xu, Q.Abresch, E.C.Axelrod, H.L.Feher, G.Okamura, M.Y.

(2005) Biochemistry 44: 6920-6928

  • DOI: https://doi.org/10.1021/bi047559m
  • Primary Citation Related Structures: 
    1YF6

  • PubMed Abstract: 

    The photosynthetic reaction center (RC) from purple bacteria converts light into chemical energy. Although the RC shows two nearly structurally symmetric branches, A and B, light-induced electron transfer in the native RC occurs almost exclusively along the A-branch to a primary quinone electron acceptor Q(A). Subsequent electron and proton transfer to a mobile quinone molecule Q(B) converts it to a quinol, Q(B)H(2). We report the construction and characterization of a series of mutants in Rhodobacter sphaeroides designed to reduce Q(B) via the B-branch. The quantum efficiency to Q(B) via the B-branch Phi(B) ranged from 0.4% in an RC containing the single mutation Ala-M260 --> Trp to 5% in a quintuple mutant which includes in addition three mutations to inhibit transfer along the A-branch (Gly-M203 --> Asp, Tyr-M210 --> Phe, Leu-M214 --> His) and one to promote transfer along the B-branch (Phe-L181 --> Tyr). Comparing the value of 0.4% for Phi(B) obtained in the AW(M260) mutant, which lacks Q(A), to the 100% quantum efficiency for Phi(A) along the A-branch in the native RC, we obtain a ratio for A-branch to B-branch electron transfer of 250:1. We determined the structure of the most effective (quintuple) mutant RC at 2.25 A (R-factor = 19.6%). The Q(A) site did not contain a quinone but was occupied by the side chain of Trp-M260 and a Cl(-). In this structure a nonfunctional quinone was found to occupy a new site near M258 and M268. The implications of this work to trap intermediate states are discussed.


  • Organizational Affiliation
    • Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. mpaddock@physics.ucsd.edu

Macromolecule Content 

  • Total Structure Weight: 105.29 kDa 
  • Atom Count: 7,450 
  • Modeled Residue Count: 820 
  • Deposited Residue Count: 848 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]281Cereibacter sphaeroidesMutation(s): 1 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]307Cereibacter sphaeroidesMutation(s): 4 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
V [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL

Query on BCL



Download:Ideal Coordinates CCD File
D [auth L],
E [auth L],
Q [auth M],
R [auth M],
S [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
F [auth L]BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10

Query on U10



Download:Ideal Coordinates CCD File
G [auth L],
H [auth L],
T [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPO

Query on SPO



Download:Ideal Coordinates CCD File
U [auth M]SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
J [auth L],
K [auth L],
W [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO

Query on HTO



Download:Ideal Coordinates CCD File
I [auth L]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
O [auth M],
P [auth M]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
M
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth M]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.216 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.442α = 90
b = 139.442β = 90
c = 185.46γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description