7Q7Q

LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 

wwPDB Validation   3D Report Full Report


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Literature

Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre.

Bath, P.Banacore, A.Borjesson, P.Bosman, R.Wickstrand, C.Safari, C.Dods, R.Ghosh, S.Dahl, P.Ortolani, G.Bjorg Ulfarsdottir, T.Hammarin, G.Garcia Bonete, M.J.Vallejos, A.Ostojic, L.Edlund, P.Linse, J.B.Andersson, R.Nango, E.Owada, S.Tanaka, R.Tono, K.Joti, Y.Nureki, O.Luo, F.James, D.Nass, K.Johnson, P.J.M.Knopp, G.Ozerov, D.Cirelli, C.Milne, C.Iwata, S.Branden, G.Neutze, R.

(2022) Acta Crystallogr D Struct Biol 78: 698-708

  • DOI: 10.1107/S2059798322004144
  • Primary Citation of Related Structures:  
    7Q7P, 7Q7Q

  • PubMed Abstract: 
  • Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described ...

    Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile Q B pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.


    Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth CCC]336Blastochloris viridisMutation(s): 0 
Gene Names: pufCcytCBVIRIDIS_00500
UniProt
Find proteins for P07173 (Blastochloris viridis)
Explore P07173 
Go to UniProtKB:  P07173
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07173
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein H chainB [auth HHH]258Blastochloris viridisMutation(s): 0 
Gene Names: puhA
UniProt
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Entity Groups  
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UniProt GroupP06008
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein L chainC [auth LLL]273Blastochloris viridisMutation(s): 0 
Gene Names: pufL
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups  
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UniProt GroupP06009
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein M chainD [auth MMM]323Blastochloris viridisMutation(s): 0 
Gene Names: pufM
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06010
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

Download Ideal Coordinates CCD File 
AA [auth MMM],
M [auth LLL],
N [auth LLL],
Z [auth MMM]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
BPB
Query on BPB

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BA [auth MMM],
O [auth LLL]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
MQ9
Query on MQ9

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Y [auth MMM]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
 Ligand Interaction
DGA
Query on DGA

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I [auth CCC]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
 Ligand Interaction
HEC
Query on HEC

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E [auth CCC],
F [auth CCC],
G [auth CCC],
H [auth CCC]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
NS5
Query on NS5

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CA [auth MMM]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
OLC
Query on OLC

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FA [auth MMM],
JA [auth MMM]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
UQ2
Query on UQ2

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LA [auth MMM],
U [auth LLL]
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
LDA
Query on LDA

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EA [auth MMM],
GA [auth MMM],
HA [auth MMM],
IA [auth MMM],
J [auth HHH],
EA [auth MMM],
GA [auth MMM],
HA [auth MMM],
IA [auth MMM],
J [auth HHH],
K [auth HHH],
X [auth MMM]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

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DA [auth MMM],
KA [auth MMM],
P [auth LLL],
Q [auth LLL],
R [auth LLL],
DA [auth MMM],
KA [auth MMM],
P [auth LLL],
Q [auth LLL],
R [auth LLL],
S [auth LLL],
T [auth LLL],
V [auth LLL]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
SO4
Query on SO4

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L [auth HHH],
MA [auth MMM],
NA [auth MMM],
OA [auth MMM],
PA [auth MMM]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

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W [auth MMM]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
B [auth HHH]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.66α = 90
b = 125.13β = 90
c = 182.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Development and Innovation Office (NKFIH)European Union789030
European Research Council (ERC)Sweden2015-00560

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release