4HBJ | pdb_00004hbj

Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265 replaced with GLN

• PDB DOI: https://doi.org/10.2210/pdb4HBJ/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Cereibacter sphaeroides
• Expression System: Cereibacter sphaeroides
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2012-09-28 Released: 2013-01-23 
• Deposition Author(s): Mattis, A.J., Wraight, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides

Mattis, A.J., Wraight, C.A.

To be published.

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: 102.43 kDa 
• Atom Count: 6,988 
• Modeled Residue Count: 822 
• Deposited Residue Count: 854 
• 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  Gene Names: pufL 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]	313	Cereibacter sphaeroides	Mutation(s): 1  Gene Names: pufM 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCL	D [auth L], E [auth L], H [auth M], J [auth M]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPH	F [auth L], K [auth M]	BACTERIOPHEOPHYTIN A C55 H76 N4 O6 KWOZSBGNAHVCKG-SZQBJALDSA-N
U10	G [auth L], L [auth M]	UBIQUINONE-10 C59 H90 O4 ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPO	M	SPHEROIDENE C41 H60 O FJOCMTHZSURUFA-KXCOHNEYSA-N
FE	I [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.54	α = 90
b = 139.54	β = 90
c = 185.07	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Mattis, A.J., Wraight, C.A.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description