4CAS

Serial femtosecond crystallography structure of a photosynthetic reaction center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

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.H.Schlichting, I.Chapman, H.N.Fromme, P.Neutze, R.

(2013) Nat.Commun. 4: 2911

  • DOI: 10.1038/ncomms3911

  • 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 Bla ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
A
356Blastochloris viridisGene Names: pufC (cytC)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN L CHAIN
B
274Blastochloris viridisGene Names: pufL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN M CHAIN
C
324Blastochloris viridisGene Names: pufM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAIN
D
258Blastochloris viridisGene Names: puhA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
BCL
Query on BCL

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B, C
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
MPG
Query on MPG

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B, C
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
DGA
Query on DGA

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A
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
 Ligand Interaction
HEM
Query on HEM

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A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MQ7
Query on MQ7

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C
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
FE2
Query on FE2

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C
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPB
Query on BPB

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B, C
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
OTP
Query on OTP

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Download CCD File 
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
OCTAPRENYL PYROPHOSPHATE
C40 H68 O7 P2
IKKLDISSULFFQO-DJMILUHSSA-N
 Ligand Interaction
NS5
Query on NS5

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C
15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-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: 3.5 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.295 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.900α = 90.00
b = 84.800β = 90.00
c = 384.300γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata scaling
PHASERphasing
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references
  • Version 2.0: 2017-06-14
    Type: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2017-11-15
    Type: Data collection