2OZ9

E. coli TRP holorepressor, orthorhombic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flexibility of the DNA-binding domains of trp repressor.

Lawson, C.L.Zhang, R.G.Schevitz, R.W.Otwinowski, Z.Joachimiak, A.Sigler, P.B.

(1988) Proteins 3: 18-31

  • DOI: 10.1002/prot.340030103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An orthorhombic crystal form of trp repressor (aporepressor plus L-tryptophan ligand) was solved by molecular replacement, refined to 1.65 A resolution, and compared to the structure of the repressor in trigonal crystals. Even though these two crysta ...

    An orthorhombic crystal form of trp repressor (aporepressor plus L-tryptophan ligand) was solved by molecular replacement, refined to 1.65 A resolution, and compared to the structure of the repressor in trigonal crystals. Even though these two crystal forms of repressor were grown under identical conditions, the refined structures have distinctly different conformations of the DNA-binding domains. Unlike the repressor/aporepressor structural transition, the conformational shift is not caused by the binding or loss of the L-tryptophan ligand. We conclude that while L-tryptophan binding is essential for forming a specific complex with trp operator DNA, the corepressor ligand does not lock the repressor into a single conformation that is complementary to the operator. This flexibility may be required by the various binding modes proposed for trp repressor in its search for and adherence to its three different operator sites.


    Related Citations: 
    • Nucleotide Sequence and Expression of Escherichia Coli Trpr, the Structural Gene for the Trp Aporepressor
      Gunsalus, R.P.,Yanofsky, C.
      (1980) Proc.Natl.Acad.Sci.USA 77: 7117
    • The Crystal Structure of Trp Aporepressor at 1.8 Angstroms Shows How Binding Tryptophan Enhances DNA Affinity
      Zhang, R.G.,Joachimiak, A.,Lawson, C.L.,Schevitz, R.W.,Otwinowski, Z.,Sigler, P.B.
      (1987) Nature 327: 891
    • Functional Inferences from Crystals of Escherichia Coli Trp Repressor
      Joachimiak, A.,Schevitz, R.W.,Kelley, R.L.,Yanofsky, C.,Sigler, P.B.
      (1983) J.Biol.Chem. 258: 12641
    • The Three-Dimensional Structure of Trp Repressor
      Schevitz, R.W.,Otwinowski, Z.,Joachimiak, A.,Lawson, C.L.,Sigler, P.B.
      (1985) Nature 317: 782
    • Purification and Characterization of Trp Repressor
      Joachimiak, A.,Kelley, R.L.,Gunsalus, R.P.,Yanofsky, C.,Sigler, P.B.
      (1983) Proc.Natl.Acad.Sci.USA 80: 668


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trp operon repressor
R
107Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: trpR (rtrY)
Find proteins for P0A881 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A881
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
R
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TRP
Query on TRP

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Download CCD File 
R
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.300α = 90.00
b = 53.600β = 90.00
c = 33.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MERLOTphasing
PROFFTrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance