8C87

Double mutant A(L172)C/L(L246)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds.

Selikhanov, G.Atamas, A.Yukhimchuk, D.Fufina, T.Vasilieva, L.Gabdulkhakov, A.

(2023) Membranes (Basel) 13

  • DOI: https://doi.org/10.3390/membranes13020154
  • Primary Citation of Related Structures:  
    8C5X, 8C6K, 8C7C, 8C87, 8C88

  • PubMed Abstract: 

    The photosynthetic reaction center of the purple nonsulfur bacterium Cereibacter sphaeroides is a useful model for the study of mechanisms of photoinduced electron transfer and a promising component for photo-bio-electrocatalytic systems. The basic research and technological applications of this membrane pigment-protein complex require effective approaches to increase its structural stability. In this work, a rational design approach to genetically modify the reaction centers by introducing disulfide bonds is used. This resulted in significantly increasing the thermal stability of some of the mutant pigment-protein complexes. The formation of the S-S bonds was confirmed by X-ray crystallography as well as SDS-PAGE, and the optical properties of the reaction centers were studied. The genetically modified reaction centers presented here preserved their ability for photochemical charge separation and could be of interest for basic science and biotechnology.


  • Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainA [auth H]251Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: puhA
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]281Cereibacter sphaeroides 2.4.1Mutation(s): 3 
Gene Names: pufL
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]303Cereibacter sphaeroides 2.4.1Mutation(s): 1 
Gene Names: pufM
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
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  • 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 (Subject of Investigation/LOI)
Query on BCL

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L,
M [auth L],
N [auth L],
W [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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O [auth L],
X [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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Z [auth M]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPN (Subject of Investigation/LOI)
Query on SPN

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AA [auth M]SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
OLC (Subject of Investigation/LOI)
Query on OLC

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K [auth L](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
LDA
Query on LDA

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BA [auth M]
CA [auth M]
D [auth H]
DA [auth M]
EA [auth M]
BA [auth M],
CA [auth M],
D [auth H],
DA [auth M],
EA [auth M],
H,
HA [auth M],
I [auth H],
IA [auth M],
J [auth H],
P [auth L],
U [auth L]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO
Query on HTO

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S [auth L],
T [auth L]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
EDO
Query on EDO

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G [auth H],
GA [auth M]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

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Y [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
UNL
Query on UNL

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E [auth H],
F [auth H],
FA [auth M],
Q [auth L],
R [auth L]
Unknown ligand
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.725α = 90
b = 99.725β = 90
c = 239.107γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation18-02-40008

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release