1EFA | pdb_00001efa

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 (Depositor) 
  • R-Value Work: 
    0.247 (Depositor) 
  • R-Value Observed: 
    0.247 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.2 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: https://doi.org/10.1038/73317
  • Primary Citation 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 (4.8 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.

    • 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.

Macromolecule Content 

  • Total Structure Weight: 121.05 kDa 
  • Atom Count: 7,838 
  • Modeled Residue Count: 978 
  • Deposited Residue Count: 1,041 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03023
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

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

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
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2024-02-07
    Changes: Data collection