5MVV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

wwPDB Validation 3D Report Full Report


This is version 2.2 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
  • Structures With Same Primary Citation

  • 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-1A378Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PFL2215w
Find proteins for Q8I4X0 (Plasmodium falciparum (isolate 3D7))
Explore Q8I4X0 
Go to UniProtKB:  Q8I4X0
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GelsolinG127Mus musculusMutation(s): 0 
Gene Names: GsnGsb
Find proteins for P13020 (Mus musculus)
Explore P13020 
Go to UniProtKB:  P13020
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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

Download CCD File 
A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.42α = 90
b = 68.92β = 90
c = 71.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 2.0: 2017-07-19
    Changes: Atomic model
  • Version 2.1: 2017-08-02
    Changes: Database references
  • Version 2.2: 2019-10-16
    Changes: Data collection