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 

Starting Model: experimental
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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 2.8 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
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT356Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN L CHAIN274Blastochloris viridisMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN M CHAIN324Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN H CHAIN258Blastochloris viridisMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / 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-AGGZHOMASA-M
BPB
Query on BPB

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M [auth B],
R [auth C]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
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
MQ7
Query on MQ7

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S [auth C]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
DGA
Query on DGA

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I [auth A]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
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
NS5
Query on NS5

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T [auth C]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
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
PO4
Query on PO4

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W [auth C],
X [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE2
Query on FE2

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P [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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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Ligand Structure Quality Assessment 


Entry History 

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
  • Version 3.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description