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: 8.2 Å
  • R-Value Free: 0.384 
  • R-Value Work: 0.351 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nmeth.1867

  • 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 micr ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
C
336Blastochloris viridisMutation(s): 0 
Gene Names: pufC (cytC)
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAIN
H
258Blastochloris viridisMutation(s): 0 
Gene Names: puhA
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN L CHAIN
L
274Blastochloris viridisMutation(s): 0 
Gene Names: pufL
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN M CHAIN
M
324Blastochloris viridisMutation(s): 0 
Gene Names: pufM
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MQ7
Query on MQ7

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Download CCD File 
M
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
M
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPB
Query on BPB

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Download CCD File 
L, M
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
BCB
Query on BCB

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Download CCD File 
L, M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
NS5
Query on NS5

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Download CCD File 
M
15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
H, M
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.2 Å
  • R-Value Free: 0.384 
  • R-Value Work: 0.351 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.500α = 90.00
b = 84.600β = 90.00
c = 375.800γ = 90.00
Software Package:
Software NamePurpose
MONTEdata scaling
CrystFELdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History