1EFA

CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A closer view of the conformation of the Lac repressor bound to operator.

Bell, C.E.Lewis, M.

(2000) Nat Struct Biol 7: 209-214

  • DOI: 10.1038/73317
  • Primary Citation of Related Structures:  
    1EFA

  • PubMed Abstract: 
  • Crystal structures of the Lac repressor, with and without isopropyithiogalactoside (IPTG), and the repressor bound to operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the operator. However, because of the low resolution of the operator-bound structure (4 ...

    Crystal structures of the Lac repressor, with and without isopropyithiogalactoside (IPTG), and the repressor bound to operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the operator. However, because of the low resolution of the operator-bound structure (4.8 A), the model for the allosteric transition was presented in terms of structural elements rather than in terms of side chain interactions. Here we have constructed a dimeric Lac repressor and determined its structure at 2.6 A resolution in complex with a symmetric operator and the anti-inducer orthonitrophenylfucoside (ONPF). The structure enables the induced (IPTG-bound) and repressed (operator-bound) conformations of the repressor to be compared in atomic detail. An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition.


    Related Citations: 
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
      Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C.
      (1996) Science 271: 1247
    • Crystal structure of lac repressor core tetramer and its implications for DNA looping
      Friedman, A.M., Fischmann, T.O., Steitz, T.A.
      (1995) Science 268: 1721
    • The solution structure of lac repressor headpiece 62 complexed to a symmetrical lac operator sequence determined by NMR and restrained molecular dynamics
      Spronk, C.A.E.M., Bonvin, A.M.J.J., Radha, P.K., Melacini, G., Boelens, R.
      (1999) Structure 7: 1483
    • Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator
      Slijper, M., Bonvin, A.M., Boelens, R., Kaptein, R.
      (1996) J Mol Biol 259: 761

    Organizational Affiliation

    The Johnson Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton walk, Philadelphia, Pennsylvania 19102-6059, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LAC REPRESSORC [auth A], D [auth B], E [auth C]333Escherichia coliMutation(s): 1 
UniProt
Find proteins for P03023 (Escherichia coli (strain K12))
Explore P03023 
Go to UniProtKB:  P03023
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')A [auth D], B [auth E]21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPF (Subject of Investigation/LOI)
Query on NPF

Download Ideal Coordinates CCD File 
F [auth A], G [auth B], H [auth C]2-nitrophenyl beta-D-fucopyranoside
C12 H15 N O7
SWRPIVXPHLYETN-BVWHHUJWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 251.438α = 90
b = 251.438β = 90
c = 204.791γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2000-02-07 
  • Released Date: 2000-03-06 
  • Deposition Author(s): Bell, C.E., Lewis, M.

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary