2JBL | pdb_00002jbl

PHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS

• PDB DOI: https://doi.org/10.2210/pdb2JBL/pdb
• Entry: 2JBL supersedes: 4PRC

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


• Deposited: 2006-12-08 Released: 2007-03-13 
• Deposition Author(s): Lancaster, C.R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.206 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex.

Lancaster, C.R.D., Hunte, C., Kelley, J., Trumpower, B.L., Ditchfield, R.

(2007) J Mol Biology 368: 197

• PubMed: 17337272 
• DOI: https://doi.org/10.1016/j.jmb.2007.02.013
• Primary Citation Related Structures: 
  2IBZ, 2JBL


• PubMed Abstract: 
  

  We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.

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Organizational Affiliation: 
• Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany. [e-mail]

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 145.79 kDa 
• Atom Count: 10,512 
• Modeled Residue Count: 1,186 
• Deposited Residue Count: 1,210 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT	A [auth C]	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 H CHAIN	B [auth H]	258	Blastochloris viridis	Mutation(s): 0  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  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  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	K [auth L], L, O [auth L], P [auth M]	BACTERIOCHLOROPHYLL B C55 H72 Mg N4 O6 QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB	M [auth L], Q [auth M]	BACTERIOPHEOPHYTIN B C55 H74 N4 O6 SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7	S [auth M]	MENAQUINONE-7 C46 H64 O2 RAKQPZMEYJZGPI-LJWNYQGCSA-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	T [auth M]	15-cis-1,2-dihydroneurosporene C40 H60 NHKJSVKSSGKUCH-DBWJSHEJSA-N
SMA	N [auth L]	STIGMATELLIN A C30 H42 O7 UZHDGDDPOPDJGM-WPPYOTIYSA-N
LDA	I [auth H], U [auth M], V [auth M], W [auth M], X [auth M], Y [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
SO4	AA [auth M], BA [auth M], J [auth H], Z [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	R [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-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: 2.40 Å
• R-Value Free:  0.206 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.5	α = 90
b = 223.5	β = 90
c = 113.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Lancaster, C.R.D.
• This entry supersedes: 4PRC

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2012-02-01
  Changes: Derived calculations, Non-polymer description, Version format compliance
• Version 1.2: 2014-10-22
  Changes: Database references
• Version 1.3: 2019-07-24
  Changes: Advisory, Data collection, Derived calculations
• Version 2.0: 2019-09-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary