4HYJ

Crystal structure of Exiguobacterium sibiricum rhodopsin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria.

Gushchin, I., Chervakov, P., Kuzmichev, P., Popov, A.N., Round, E., Borshchevskiy, V., Ishchenko, A., Petrovskaya, L., Chupin, V., Dolgikh, D.A., Arseniev, A.A., Kirpichnikov, M., Gordeliy, V.

(2013) Proc Natl Acad Sci U S A 110: 12631-12636

  • DOI: 10.1073/pnas.1221629110
  • Primary Citation of Related Structures:  
    4HYJ

  • PubMed Abstract: 

    • Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features ...

    Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features. First, ESR's proton donor is a lysine side chain that is situated very close to the bulk solvent. Second, the α-helical structure in the middle of the helix F is replaced by 3(10)- and π-helix-like elements that are stabilized by the Trp-154 and Asn-224 side chains. This feature is characteristic for the proteorhodopsin family of proteins. Third, the proton release region is connected to the bulk solvent by a chain of water molecules already in the ground state. Despite these peculiarities, the positions of water molecule and amino acid side chains in the immediate Schiff base vicinity are very well conserved. These features make ESR a very unusual proton pump. The presented structure sheds light on the large family of proteorhodopsins, for which structural information was not available previously.

    Organizational Affiliation: 

    Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, 38027 Grenoble, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhodopsinA, B258Exiguobacterium sibiricumMutation(s): 0 
Gene Names: Exig_1419
Membrane Entity: Yes 
UniProt
Find proteins for B1YFV8 (Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 / 255-15))
Explore B1YFV8 
Go to UniProtKB:  B1YFV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1YFV8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET
Download Ideal Coordinates CCD File 
C [auth A],
P [auth B]		RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N		 Ligand Interaction
LFA
Query on LFA
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.099α = 90
b = 96.099β = 90
c = 124.38γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references