5LRI

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH TRP (CHAIN L, EL212W)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 ?
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

On the mechanism of ubiquinone mediated photocurrent generation by a reaction center based photocathode.

Friebe, V.M.Swainsbury, D.J.Fyfe, P.K.van der Heijden, W.Jones, M.R.Frese, R.N.

(2016) Biochim Biophys Acta 1857: 1925-1934

  • DOI: https://doi.org/10.1016/j.bbabio.2016.09.011
  • Primary Citation of Related Structures:  
    5LRI, 5LSE

  • PubMed Abstract: 

    Upon photoexcitation, the reaction center (RC) pigment-proteins that facilitate natural photosynthesis achieve a metastable separation of electrical charge among the embedded cofactors. Because of the high quantum efficiency of this process, there is a growing interest in their incorporation into biohybrid materials for solar energy conversion, bioelectronics and biosensing. Multiple bioelectrochemical studies have shown that reaction centers from various photosynthetic organisms can be interfaced with diverse electrode materials for the generation of photocurrents, but many mechanistic aspects of native protein functionality in a non-native environment is unknown. In vivo, RC's catalyse ubiquinone-10 reduction, protonation and exchange with other lipid phase ubiquinone-10s via protein-controlled spatial orientation and protein rearrangement. In contrast, the mechanism of ubiquinone-0 reduction, used to facilitate fast RC turnover in an aqueous photoelectrochemical cell (PEC), may not proceed via the same pathway as the native cofactor. In this report we show truncation of the native isoprene tail results in larger RC turnover rates in a PEC despite the removal of the tail's purported role of ubiquinone headgroup orientation and binding. Through the use of reaction centers with single or double mutations, we also show the extent to which two-electron/two-proton ubiquinone chemistry that operates in vivo also underpins the ubiquinone-0 reduction by surface-adsorbed RCs in a PEC. This reveals that only the ubiquinone headgroup is critical to the fast turnover of the RC in a PEC and provides insight into design principles for the development of new biophotovoltaic cells and biosensors.


  • Organizational Affiliation

    Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081, HV, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]281Cereibacter sphaeroides 2.4.1Mutation(s): 1 
Gene Names: pufLRHOS4_18610RSP_0257
Membrane Entity: Yes 
UniProt
Find proteins for Q3J1A5 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J1A5 
Go to UniProtKB:  Q3J1A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J1A5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]307Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: pufMRHOS4_18600RSP_0256
Membrane Entity: Yes 
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J1A6 
Go to UniProtKB:  Q3J1A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J1A6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H]260Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: puhARHOS4_18960RSP_0291
Membrane Entity: Yes 
UniProt
Find proteins for Q3J170 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J170 
Go to UniProtKB:  Q3J170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J170
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
R [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

Download Ideal Coordinates CCD File 
D [auth L],
L [auth M],
M,
N [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

Download Ideal Coordinates CCD File 
E [auth L],
O [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10
Query on U10

Download Ideal Coordinates CCD File 
F [auth L],
P [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPN
Query on SPN

Download Ideal Coordinates CCD File 
Q [auth M]SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
LDA
Query on LDA

Download Ideal Coordinates CCD File 
I [auth M],
J [auth M],
K [auth M],
S [auth M],
T [auth H]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
DD9
Query on DD9

Download Ideal Coordinates CCD File 
G [auth L],
U [auth H],
V [auth H]
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
H [auth L]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 ?
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 139.82¦Á = 90
b = 139.82¦Â = 90
c = 185.252¦Ã = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I022570/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomB13439

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
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