1EFC

INTACT ELONGATION FACTOR FROM E.COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution.

Song, H.Parsons, M.R.Rowsell, S.Leonard, G.Phillips, S.E.

(1999) J.Mol.Biol. 285: 1245-1256

  • DOI: 10.1006/jmbi.1998.2387

  • PubMed Abstract: 
  • The crystal structure of intact elongation factor Tu (EF-Tu) from Escherichia coli in GDP-bound conformation has been determined using a combination of multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction (MAD) methods. Th ...

    The crystal structure of intact elongation factor Tu (EF-Tu) from Escherichia coli in GDP-bound conformation has been determined using a combination of multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction (MAD) methods. The current atomic model has been refined to a crystallographic R factor of 20.3 % and free R-factor of 26.8 % in the resolution range of 10-2.05 A. The protein consists of three domains: domain 1 has an alpha/beta structure; while domain 2 and domain 3 are beta-barrel structures. Although the global fold of the current model is similar to those of published structures, the secondary structural assignment has been improved due to the high quality of the current model. The switch I region (residues 40-62) is well ordered in this structure. Comparison with the structure of EF-Tu in GDP-bound form from Thermus aquaticus shows that although the individual domain structures are similar in these two structures, the orientation of domains changes significantly. Interactions between domains 1 and 3 in our E. coli EF-Tu-GDP complex are quite different from those of EF-Tu with bound GTP from T. aquaticus, due to the domain rearrangement upon GTP binding. The binding sites of the Mg2+ and guanine nucleotide are revealed in detail. Two water molecules that co-ordinate the Mg2+ have been identified to be well conserved in the GDP and GTP-bound forms of EF-Tu structures, as well as in the structure of Ras p21 with bound GDP. Comparisons of the Mg2+ binding site with other guanine nucleotide binding proteins in GDP-bound forms show that the Mg2+ co-ordination patterns are well preserved among these structures.


    Related Citations: 
    • Helix Unwinding in the Effector Region of Elongation Factor EF-TU-Gdp
      Polekhina, G.,Thirup, S.,Kjeldgaard, M.,Nissen, P.,Lippmann, C.,Nyborg, J.
      (1996) Structure 4: 1141
    • Refined Structure of Elongation Factor EF-TU from E. Coli
      Kjeldgaard, M.,Nyborg, J.
      (1992) J.Mol.Biol. 223: 721
    • Crystal Structure of the Ternary Complex of Phe-tRNA, EF-TU and GTP Analogue
      Nissen, P.,Kjeldgaard, M.,Thirup, S.,Polekhina, G.,Reshetnikova, L.,Clark, B.F.C.,Nyborg, J.
      (1995) Science 270: 1464
    • An Alpha to Beta Conformational Switch in EF-TU
      Abel, K.,Yoder, M.D.,Hilgenfeld, R.,Jurnak, F.
      (1996) Structure 4: 1153
    • The Crystal Structure of Elongation Factor EF-TU from T. Aquaticus in the GTP Conformation
      Kjeldgaard, M.,Nissen, P.,Thirup, S.,Nyborg, J.
      (1993) Structure 1: 35


    Organizational Affiliation

    School of Biochemistry & Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ELONGATION FACTOR)
A, B
393Escherichia coli (strain K12)Gene Names: tufA
Find proteins for P0CE47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE47
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 243.120α = 90.00
b = 61.080β = 90.00
c = 66.910γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4phasing
REFMACrefinement
SCALEPACKdata scaling
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance