4CAS | pdb_00004cas

Serial femtosecond crystallography structure of a photosynthetic reaction center

• PDB DOI: https://doi.org/10.2210/pdb4CAS/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Blastochloris viridis
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2013-10-09 Released: 2013-12-25 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.329 (Depositor), 0.325 (DCC) 
• R-Value Work: 
  0.295 (Depositor), 0.296 (DCC) 
• R-Value Observed: 
  0.296 (Depositor) 

Starting Model: experimental

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

• PubMed: 24352554 
• DOI: https://doi.org/10.1038/ncomms3911
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.
Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA.
PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA.
Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden.
Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA.
Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, 94550 California, USA.
Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA.
1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Lübeck at DESY, 22607 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 146.39 kDa 
• Atom Count: 9,890 
• Modeled Residue Count: 1,171 
• Deposited Residue Count: 1,212 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT	A	356	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173  Go to UniProtKB:  P07173

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN L CHAIN	B	274	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009  Go to UniProtKB:  P06009

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN M CHAIN	C	324	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010  Go to UniProtKB:  P06010

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN H CHAIN	D	258	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008  Go to UniProtKB:  P06008

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCL	J [auth B], K [auth B], L [auth B], Q [auth C]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPB	M [auth B], R [auth C]	BACTERIOPHEOPHYTIN B C55 H74 N4 O6 SFKCKJXMIAKQMY-GTTFDWDMSA-N
OTP	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	S [auth C]	MENAQUINONE-7 C46 H64 O2 RAKQPZMEYJZGPI-LJWNYQGCSA-N
DGA	I [auth A]	DIACYL GLYCEROL C39 H76 O5 UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC	E [auth A], F [auth A], G [auth A], H [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
NS5	T [auth C]	15-cis-1,2-dihydroneurosporene C40 H60 NHKJSVKSSGKUCH-DBWJSHEJSA-N
MPG	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	W [auth C], X [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE2	P [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	D	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.329 (Depositor), 0.325 (DCC) 
• R-Value Work:  0.295 (Depositor), 0.296 (DCC) 
• R-Value Observed: 0.296 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.9	α = 90
b = 84.8	β = 90
c = 384.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): 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.

Revision History  

• 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
• Version 4.0: 2025-10-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary