3DUQ

E(L212)A, D(L213)A, N(M5)D triple mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb3DUQ/pdb

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


• Deposited: 2008-07-17 Released: 2009-06-30 
• Deposition Author(s): Pokkuluri, P.R., Schiffer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.209 

Starting Model: experimental

Literature

Structural description of compensatory mutations that restore proton transfer pathways to the L212A-L213A mutant bacterial reaction center

Pokkuluri, P.R., Laible, P.D., Ginell, S.L., Hanson, D.K., Schiffer, M.

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: 104.86 kDa 
• Atom Count: 7,261 
• Modelled Residue Count: 819 
• Deposited Residue Count: 855 
• 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): 2  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]	314	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  Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7  Go to UniProtKB:  P0C0Y7

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	P [auth M]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL	D [auth L], E [auth L], J [auth M], K [auth M]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPH	F [auth L], L [auth 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
SPN	O [auth M]	SPEROIDENONE C41 H70 O2 GWQAMGYOEYXWJF-YCDPMLDASA-N
LDA	H [auth L], I [auth L], Q [auth M], R [auth H]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
FE	M	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.209 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.3	α = 90
b = 141.3	β = 90
c = 187.4	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Pokkuluri, P.R., Schiffer, M.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description