4CAS

Serial femtosecond crystallography structure of a photosynthetic reaction center

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.296 

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Literature

Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.

Johansson, L.C., Arnlund, D., Katona, G., White, T.A., Barty, A., DePonte, D.P., Shoeman, R.L., Wickstrand, C., Sharma, A., Williams, G.J., Aquila, A., Bogan, M.J., Caleman, C., Davidsson, J., Doak, R.B., Frank, M., Fromme, R., Galli, L., Grotjohann, I., Hunter, M.S., Kassemeyer, S., Kirian, R.A., Kupitz, C., Liang, M., Lomb, L., Malmerberg, E., Martin, A.V., Messerschmidt, M., Nass, K., Redecke, L., Seibert, M.M., Sjohamn, J., Steinbrener, J., Stellato, F., Wang, D., Wahlgren, W.Y., Weierstall, U., Westenhoff, S., Zatsepin, N.A., Boutet, S., Spence, J.C., Schlichting, I., Chapman, H.N., Fromme, P., Neutze, R.

(2013) Nat Commun 4: 2911-2911

  • DOI: https://doi.org/10.1038/ncomms3911
  • Primary Citation of Related Structures:  
    4CAS

  • PubMed Abstract: 

    • Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2 ...

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

    Organizational Affiliation: 

    Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT356Blastochloris viridisMutation(s): 0 
Gene Names: pufC, cytC, BVIRIDIS_00500
Membrane Entity: Yes 
UniProt
Find proteins for P07173 (Blastochloris viridis)
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Go to UniProtKB:  P07173
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07173
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN L CHAIN274Blastochloris viridisMutation(s): 0 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06009
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN M CHAIN324Blastochloris viridisMutation(s): 0 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
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Entity Groups  
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UniProt GroupP06010
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN H CHAIN258Blastochloris viridisMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06008
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL
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J [auth B],
K [auth B],
L [auth B],
Q [auth C]		BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ		 Ligand Interaction
BPB
Query on BPB
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M [auth B],
R [auth C]		BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N		 Ligand Interaction
OTP
Query on OTP
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U [auth C](2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
C40 H68 O7 P2
IKKLDISSULFFQO-DJMILUHSSA-N		 Ligand Interaction
MQ7
Query on MQ7
Download Ideal Coordinates CCD File 
S [auth C]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N		 Ligand Interaction
DGA
Query on DGA
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I [auth A]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N		 Ligand Interaction
HEC
Query on HEC
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E [auth A],
F [auth A],
G [auth A],
H [auth A]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
NS5
Query on NS5
Download Ideal Coordinates CCD File 
T [auth C]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N		 Ligand Interaction
MPG
Query on MPG
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N [auth B],
O [auth B],
V [auth C]		[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N		 Ligand Interaction
PO4
Query on PO4
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W [auth C],
X [auth C]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
FE2
Query on FE2
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P [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
D
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.296 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.9α = 90
b = 84.8β = 90
c = 384.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 2.0: 2017-06-14
    Changes: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2017-11-15
    Changes: Data collection
  • Version 2.2: 2018-09-19
    Changes: Data collection, Database references
  • Version 2.3: 2018-11-14
    Changes: Data collection
  • Version 3.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2019-09-04
    Changes: Data collection