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crystal structure of the essential E. coli YeaZ protein by MAD method using the gadolinium complex "DOTMA"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Complement to the Modern Crystallographer'S Toolbox: Caged Gadolinium Complexes with Versatile Binding Modes.

Stelter, M.Molina, R.Jeudy, S.Kahn, R.Abergel, C.Hermoso, J.A.

(2014) Acta Crystallogr.,Sect.D 70: 1506

  • DOI: 10.1107/S1399004714005483

  • PubMed Abstract: 
  • A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd(3+) ion into protein crystals in order to provide strong anomalous scattering for de novo phasing. The complexes contained multidentate ligand molecules wi ...

    A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd(3+) ion into protein crystals in order to provide strong anomalous scattering for de novo phasing. The complexes contained multidentate ligand molecules with different functional groups to provide a panel of possible interactions with the protein. An exhaustive crystallographic analysis showed them to be nondisruptive to the diffraction quality of the prepared derivative crystals, and as many as 50% of the derivatives allowed the determination of accurate phases, leading to high-quality experimental electron-density maps. At least two successful derivatives were identified for all tested proteins. Structure refinement showed that the complexes bind to the protein surface or solvent-accessible cavities, involving hydrogen bonds, electrostatic and CH-π interactions, explaining their versatile binding modes. Their high phasing power, complementary binding modes and ease of use make them highly suitable as a heavy-atom screen for high-throughput de novo structure determination, in combination with the SAD method. They can also provide a reliable tool for the development of new methods such as serial femtosecond crystallography.


    Related Citations: 
    • Preliminary Crystallographic Analysis of the Escherichia Coli Yeaz Protein Using the Anomalous Signal of a Gadolinium Derivative.
      Jeudy, S.,Stelter, M.,Coutard, B.,Kahn, R.,Abergel, C.
      (2005) Acta Crystallogr.,Sect.F 61: 848


    Organizational Affiliation

    University Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
A, B, C, D
251Escherichia coli (strain K12)Gene Names: tsaB (yeaZ)
Find proteins for P76256 (Escherichia coli (strain K12))
Go to UniProtKB:  P76256
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD3
Query on GD3

Download SDF File 
Download CCD File 
A
GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.340α = 90.00
b = 97.600β = 90.00
c = 141.940γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-16
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2014-07-23
    Type: Database references, Other, Structure summary