4AC5

Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.20 Å
  • R-Value Free: 0.384 
  • R-Value Work: 0.351 
  • R-Value Observed: 0.352 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Lipidic Phase Membrane Protein Serial Femtosecond Crystallography.

Johansson, L.C.Arnlund, D.White, T.A.Katona, G.Deponte, D.P.Weierstall, U.Doak, R.B.Shoeman, R.L.Lomb, L.Malmerberg, E.Davidsson, J.Nass, K.Liang, M.Andreasson, J.Aquila, A.Bajt, S.Barthelmess, M.Barty, A.Bogan, M.J.Bostedt, C.Bozek, J.D.Caleman, C.Coffee, R.Coppola, N.Ekeberg, T.Epp, S.W.Erk, B.Fleckenstein, H.Foucar, L.Graafsma, H.Gumprecht, L.Hajdu, J.Hampton, C.Y.Hartmann, R.Hartmann, A.Hauser, G.Hirsemann, H.Holl, P.Hunter, M.S.Kassemeyer, S.Kimmel, N.Kirian, R.A.Maia, F.R.N.C.Marchesini, S.Martin, A.V.Reich, C.Rolles, D.Rudek, B.Rudenko, A.Schlichting, I.Schulz, J.Seibert, M.M.Sierra, R.Soltau, H.Starodub, D.Stellato, F.Stern, S.Struder, L.Timneanu, N.Ullrich, J.Wahlgren, W.Y.Wang, X.Weidenspointner, G.Wunderer, C.Fromme, P.Chapman, H.N.Spence, J.C.H.Neutze, R.

(2012) Nat Methods 9: 263

  • DOI: https://doi.org/10.1038/nmeth.1867
  • Primary Citation of Related Structures:  
    4AC5

  • PubMed Abstract: 

    X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNITA [auth C]336Blastochloris 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 H CHAINB [auth H]258Blastochloris 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN L CHAINC [auth L]274Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups  
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UniProt GroupP06009
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN M CHAIND [auth M]324Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups  
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UniProt GroupP06010
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

Download Ideal Coordinates CCD File 
I [auth L],
J [auth L],
L [auth M],
M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB
Query on BPB

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

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P [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
HEM
Query on HEM

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E [auth C],
F [auth C],
G [auth C],
H [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NS5
Query on NS5

Download Ideal Coordinates CCD File 
Q [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
O [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
B [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.20 Å
  • R-Value Free: 0.384 
  • R-Value Work: 0.351 
  • R-Value Observed: 0.352 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.5α = 90
b = 84.6β = 90
c = 375.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
MONTEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Other
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2018-02-14
    Changes: Data collection
  • Version 1.4: 2018-11-14
    Changes: Data collection
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description