1S00 | pdb_00001s00

PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-SEPARATED D+QAQB- STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.268 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.str.2004.03.001
  • Primary Citation Related Structures: 
    1RVJ, 1RY5, 1RZH, 1RZZ, 1S00

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 203.29 kDa 
  • Atom Count: 14,144 
  • Modeled Residue Count: 1,654 
  • Deposited Residue Count: 1,696 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L],
D [auth R]
281Cereibacter sphaeroidesMutation(s): 1 
Gene Names: PUFL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M],
E [auth S]
307Cereibacter sphaeroidesMutation(s): 1 
Gene Names: PUFM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H],
F [auth T]
260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: PUHA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL

Query on BCL



Download:Ideal Coordinates CCD File
G [auth L]
H [auth L]
I [auth L]
M
R
G [auth L],
H [auth L],
I [auth L],
M,
R,
V [auth S],
W [auth S],
X [auth S]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
J [auth L],
N [auth M],
S [auth R],
Y [auth S]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10

Query on U10



Download:Ideal Coordinates CCD File
K [auth L],
O [auth M],
T [auth R],
Z [auth S]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPO

Query on SPO



Download:Ideal Coordinates CCD File
AA [auth S],
P [auth M]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
Q [auth M]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
L [auth M],
U [auth S]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.268 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.731α = 90
b = 137.731β = 90
c = 277.153γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description