Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 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: 104.17 kDa 
• Atom Count: 7586 
• Residue Count: 820 
• Unique protein chains: 3

1RZH

PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-NEUTRAL DQAQB STATE (TRIGONAL FORM)

• DOI: 10.2210/pdb1RZH/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Rhodobacter sphaeroides
• Expression System: Rhodobacter sphaeroides
• Mutation(s): Yes 


• Deposited: 2003-12-24 Released: 2004-04-13 
• Deposition Author(s): Xu, Q., Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. sphaeroides; Altered Proton Transfer Pathways.

Xu, Q., Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.

(2004) Structure 12: 703-715

• PubMed: 15062092 
• DOI: 10.1016/j.str.2004.03.001
• Structures With Same Primary Citation


• PubMed Abstract: 
  

In the photosynthetic reaction center (RC) from Rhodobacter sphaeroides, the reduction of a bound quinone molecule Q(B) is coupled with proton uptake. When Asp-L213 is replaced by Asn, proton transfer is inhibited. Proton transfer was restored by two second-site revertant mutations, Arg-M233-->Cys and Arg-H177-->His. Kinetic effects of Cd(2+) on proton transfer showed that the entry point in revertant RCs to be the same as in the native RC. The structures of the parental and two revertant RCs were determined at resolutions of 2.10, 1.80, and 2.75 A. From the structures, we were able to delineate alternate proton transfer pathways in the revertants. The main changes occur near Glu-H173, which allow it to substitute for the missing Asp-L213. The electrostatic changes near Glu-H173 cause it to be a good proton donor and acceptor, and the structural changes create a cavity which accommodates water molecules that connect Glu-H173 to other proton transfer components.

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Related Citations: 

• Characterization of Second Site Mutations Show that Fast Proton Transfer to Qb- is Restored in Bacterial Reaction Centers of Rhodobacter Sphaeroides Containing the Asp-L213->Asn Lesion
  Paddock, M.L., Senft, M.E., Graige, M.S., Rongey, S.H., Turanchik, T., Feher, G., Okamura, M.Y.
  (1998) Photosynth Res 55: 281

• Determination of the Binding Sites of the Proton Transfer Inhibitors Cd2+ and Zn2+ in Bacterial Reaction Centers
  Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.
  (2000) Proc Natl Acad Sci U S A 97: 1542

• Identification of Proton Transfer Pathways in the X-Ray Crystal Structure of the Bacterial Reaction Center from Rhodobacter Sphaeroides
  Abresch, E.C., Paddock, M.L., Stowell, M.H.B., McPhillips, T.M., Axelrod, H.L., Soltis, S.M., Rees, D.C., Okamura, M.Y., Feher, G.
  (1998) Photosynth Res 55: 119

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Organizational Affiliation: 

Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Reaction center protein L chain	L	281	Rhodobacter sphaeroides	Mutation(s): 1  Gene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides) Explore P0C0Y8  Go to UniProtKB:  P0C0Y8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Reaction center protein M chain	M	307	Rhodobacter sphaeroides	Mutation(s): 1  Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides) Explore P0C0Y9  Go to UniProtKB:  P0C0Y9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Reaction center protein H chain	H	260	Rhodobacter sphaeroides	Mutation(s): 0  Gene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides) Explore P0C0Y7  Go to UniProtKB:  P0C0Y7

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	M	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL	L, M	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-RUUWGSCADZ
BPH	L, M	BACTERIOPHEOPHYTIN A C55 H76 N4 O6 KWOZSBGNAHVCKG-SZQBJALDSA-N
U10	L, M	UBIQUINONE-10 C59 H90 O4 ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPO	M	SPHEROIDENE C41 H60 O FJOCMTHZSURUFA-KXCOHNEYSA-N
LDA	H, M	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO	L	HEPTANE-1,2,3-TRIOL C7 H16 O3 HXYCHJFUBNTKQR-RNFRBKRXSA-N
PO4	M	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	M	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2	M	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.353	α = 90
b = 139.353	β = 90
c = 184.962	γ = 120

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: 2003-12-24 
• Released Date: 2004-04-13 
Deposition Author(s): Xu, Q., Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.

Revision History 

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2012-04-25
  Changes: Non-polymer description