2QTO

An anisotropic model for potassium channel KcsA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.201 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution

Chen, X.Poon, B.K.Dousis, A.Wang, Q.Ma, J.

(2007) Structure 15: 955-962

  • DOI: 10.1016/j.str.2007.06.012

  • PubMed Abstract: 
  • We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of mo ...

    We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of modes is sufficient to represent the anisotropic thermal motions in X-ray crystallographic refinement. By applying the method to potassium channel KcsA at 3.2 A, we obtained a structural model with an improved fit with the diffraction data. Moreover, the improved electron density maps allowed for large structural adjustments for 12 residues in each subunit, including the rebuilding of 3 missing side chains. Overall, the anisotropic KcsA structure at 3.2 A was systematically closer to a 2.0 A KcsA structure, especially in the selectivity filter. Furthermore, the anisotropic thermal ellipsoids from the refinement revealed functionally relevant structural flexibility. We expect this method to be a valuable tool for structural refinement of many membrane proteins with moderate-resolution diffraction data.


    Organizational Affiliation

    Graduate Program of Structural and Computational Biology and Molecular Biophysics, Rice University, Houston, TX 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Voltage-gated potassium channel
A, B, C, D
97Streptomyces lividansMutation(s): 1 
Gene Names: kcsA (skc1)
Find proteins for P0A334 (Streptomyces lividans)
Go to UniProtKB:  P0A334
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.201 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.272 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.780α = 90.00
b = 68.930β = 124.63
c = 112.040γ = 90.00
Software Package:
Software NamePurpose
SHELXSphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance