5JRF

Crystal structure of the light-driven sodium pump KR2 bound with iodide ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

Melnikov, I.Polovinkin, V.Kovalev, K.Gushchin, I.Shevtsov, M.Shevchenko, V.Mishin, A.Alekseev, A.Rodriguez-Valera, F.Borshchevskiy, V.Cherezov, V.Leonard, G.A.Gordeliy, V.Popov, A.

(2017) Sci Adv 3: e1602952-e1602952

  • DOI: 10.1126/sciadv.1602952
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a comm ...

    We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.


    Organizational Affiliation

    European Synchrotron Radiation Facility, 38043 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium pumping rhodopsin
A
288Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
Find proteins for N0DKS8 (Dokdonia eikasta)
Go to UniProtKB:  N0DKS8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
LFA
Query on LFA

Download SDF File 
Download CCD File 
A
EICOSANE
LIPID FRAGMENT
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYR
Query on LYR
A
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 40.506α = 90.00
b = 83.749β = 90.00
c = 234.102γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
SHELXDEphasing
XDSdata reduction
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release