Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer - A4B2C2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 144.04 kDa 
• Atom Count: 10747 
• Modelled Residue Count: 1186 
• Deposited Residue Count: 1186 
• Unique protein chains: 4

1VRN

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)

• PDB DOI: 10.2210/pdb1VRN/pdb
• Entry: 1VRN supersedes: 1TXW

• Classification: PHOTOSYNTHESIS
• Organism(s): Blastochloris viridis
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2005-02-23 Released: 2005-03-22 
• Deposition Author(s): Baxter, R.H.G., Seagle, B.-L., Norris, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.212 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Literature

Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark.

Baxter, R.H., Seagle, B.L., Ponomarenko, N., Norris, J.R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 605-612

• PubMed: 15858271 
• DOI: 10.1107/S0907444905005809
• Primary Citation of Related Structures:  
  1VRN


• PubMed Abstract: 
  

The structure of the Blastochloris viridis photosynthetic reaction center has been determined at 100 K by flash-freezing crystals. A data set to 2.2 A resolution provides a well determined model of the wild-type protein. Of particular interest are the position, occupancy and heterogeneity of the Q(B)-binding site. Data were also collected from a crystal frozen immediately after illumination. The data support predominant binding of Q(B) in the proximal position in both the neutral and charge-separated states.

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Related Citations: 

• Specific radiation damage illustrates light-induced structural changes in the photosynthetic reaction center
  Baxter, R.H.G., Seagle, B.-L., Ponomarenko, N., Norris, J.R.
  (2004) J Am Chem Soc 126: 16728

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Organizational Affiliation: 

Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	332	Blastochloris viridis	Mutation(s): 0  Gene Names: pufC, cytC, BVIRIDIS_00500 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 H chain	B [auth H]	258	Blastochloris viridis	Mutation(s): 1  Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008  Go to UniProtKB:  P06008

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	C [auth L]	273	Blastochloris viridis	Mutation(s): 0  Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009  Go to UniProtKB:  P06009

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	D [auth M]	323	Blastochloris viridis	Mutation(s): 0  Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010  Go to UniProtKB:  P06010

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCB	N [auth L], O [auth L], Y [auth M], Z [auth M]	BACTERIOCHLOROPHYLL B C55 H72 Mg N4 O6 QNWPCDKNPGOYNP-LQPBATPMDK
BPB	AA [auth M], P [auth L]	BACTERIOPHEOPHYTIN B C55 H74 N4 O6 SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ9	BA [auth M]	MENAQUINONE-9 C56 H80 O2 WCRXHNIUHQUASO-ABFXHILCSA-N
UQ7	Q [auth L]	UBIQUINONE-7 C44 H66 O4 DBESHHFMIFSNRV-RJYQSXAYSA-N
HEC	E [auth C], F [auth C], G [auth C], H [auth C]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
NS5	CA [auth M]	15-cis-1,2-dihydroneurosporene C40 H60 NHKJSVKSSGKUCH-DBWJSHEJSA-N
LDA	DA [auth M], EA [auth M], L [auth H], M [auth H], R [auth L], S [auth L]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
SO4	I [auth H], J [auth H], K [auth H], U [auth M], V [auth M], W [auth M], X [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	T [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.212 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 219.4	α = 90
b = 219.4	β = 90
c = 112.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-23 
• Released Date: 2005-03-22 
Deposition Author(s): Baxter, R.H.G., Seagle, B.-L., Norris, J.R.
• This entry supersedes: 1TXW

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 2.0: 2021-03-03
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary