5MVV

Crystal structure of Plasmodium falciparum actin I- gelsolin segment 1 -CdATP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Rapid cadmium SAD phasing at the standard wavelength (1 angstrom ).

Panneerselvam, S.Kumpula, E.P.Kursula, I.Burkhardt, A.Meents, A.

(2017) Acta Crystallogr D Struct Biol 73: 581-590

  • DOI: 10.1107/S2059798317006970
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins ...

    Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP-divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e. no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing.


    Organizational Affiliation

    Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-1
A
378Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I4X0 (Plasmodium falciparum)
Go to UniProtKB:  Q8I4X0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gelsolin
G
127Mus musculusMutation(s): 0 
Gene Names: Gsn (Gsb)
Find proteins for P13020 (Mus musculus)
Go to UniProtKB:  P13020
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SCN
Query on SCN

Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.129 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.420α = 90.00
b = 68.920β = 90.00
c = 71.550γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
SHELXDEphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 2.0: 2017-07-19
    Type: Atomic model
  • Version 2.1: 2017-08-02
    Type: Database references