2HJ6 | pdb_00002hj6

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylserine

• PDB DOI: https://doi.org/10.2210/pdb2HJ6/pdb

• Classification: PHOTOSYNTHESIS/MEMBRANE PROTEIN
• Organism(s): Cereibacter sphaeroides
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2006-06-30 Released: 2007-03-27 
• Deposition Author(s): Roszak, A.W., Gardiner, A.T., Isaacs, N.W., Cogdell, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Brominated Lipids Identify Lipid Binding Sites on the Surface of the Reaction Center from Rhodobacter sphaeroides.

Roszak, A.W., Gardiner, A.T., Isaacs, N.W., Cogdell, R.J.

(2007) Biochemistry 46: 2909-2916

• PubMed: 17315985 
• DOI: https://doi.org/10.1021/bi062154i
• Primary Citation Related Structures: 
  2HG3, 2HG9, 2HH1, 2HHK, 2HIT, 2HJ6


• PubMed Abstract: 
  

  This study describes the use of brominated phospholipids to distinguish between lipid and detergent binding sites on the surface of a typical alpha-helical membrane protein. Reaction centers isolated from Rhodobacter sphaeroides were cocrystallized with added brominated phospholipids. X-ray structural analysis of these crystals has revealed the presence of two lipid binding sites from the characteristic strong X-ray scattering from the bromine atoms. These results demonstrate the usefulness of this approach to mapping lipid binding sites at the surface of membrane proteins.

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Organizational Affiliation: 
• Department of Chemistry, WestCHEM.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 105.8 kDa 
• Atom Count: 7,685 
• Modeled Residue Count: 824 
• Deposited Residue Count: 848 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A [auth L]	281	Cereibacter sphaeroides	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8  Go to UniProtKB:  P0C0Y8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B [auth M]	307	Cereibacter sphaeroides	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9  Go to UniProtKB:  P0C0Y9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	C [auth H]	260	Cereibacter sphaeroides	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7  Go to UniProtKB:  P0C0Y7

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	P [auth M]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PS2	Q [auth M]	O-[{[(2R)-2-{[(9S,10S)-9,10-DIBROMOOCTADECANOYL]OXY}-3-(PALMITOYLOXY)PROPYL]OXY}(HYDROXY)PHOSPHORYL]-L-SERINE C40 H76 Br2 N O10 P HQCXPRBKTHCWQI-HQPLKVBUSA-N
BCL	D [auth L], E [auth L], K [auth M], L [auth M]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPH	F [auth L], M	BACTERIOPHEOPHYTIN A C55 H76 N4 O6 KWOZSBGNAHVCKG-SZQBJALDSA-N
U10	G [auth L], N [auth M]	UBIQUINONE-10 C59 H90 O4 ACTIUHUUMQJHFO-UPTCCGCDSA-N
LDA	AA [auth H], R [auth M], S [auth M], T [auth M], U [auth M], V [auth M], Y [auth H], Z [auth H]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO	O [auth M]	HEPTANE-1,2,3-TRIOL C7 H16 O3 HXYCHJFUBNTKQR-RNFRBKRXSA-N
PO4	I [auth M], J [auth M]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	BA [auth H], W [auth M]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	H [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
K	X [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.355	α = 90
b = 139.355	β = 90
c = 183.217	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Roszak, A.W., Gardiner, A.T., Isaacs, N.W., Cogdell, R.J.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2018-02-28
  Changes: Experimental preparation
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-04-03
  Changes: Refinement description