1JWL

Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystallographic analysis of Lac repressor bound to natural operator O1.

Bell, C.E.Lewis, M.

(2001) J Mol Biol 312: 921-926

  • DOI: 10.1006/jmbi.2001.5024
  • Primary Citation of Related Structures:  
    1JWL

  • PubMed Abstract: 
  • Previous structures of Lac repressor bound to DNA used a fully symmetric "ideal" operator sequence that is missing the central G-C base-pair present in the three natural operator sequences. Here we have determined the X-ray crystal structure of a dimeric Lac repressor bound to a 22 base-pair DNA with the natural operator O1 sequence and the anti-inducer ONPF, at 4 ...

    Previous structures of Lac repressor bound to DNA used a fully symmetric "ideal" operator sequence that is missing the central G-C base-pair present in the three natural operator sequences. Here we have determined the X-ray crystal structure of a dimeric Lac repressor bound to a 22 base-pair DNA with the natural operator O1 sequence and the anti-inducer ONPF, at 4.0 A resolution. The natural operator is bent in the same way as the symmetric sequence, due to the binding of the hinge helices of the repressor to the minor groove at the central GCGG sequence of O1. Comparison of the structures of the repressor bound to the natural and symmetric operators shows very similar overall structures, with only slight rearrangements of the headpiece domains of the repressor. Analysis of crystals with iodinated DNA shows that the operator is uniquely positioned and allows for the sequence registration of the DNA relative to the repressor to be determined. The kink in the operator is centered between the left half-site and the central G-C base-pair of O1. Our results are most consistent with a previously proposed model in which, relative to the complex with the symmetric operator, the repressor accommodates binding to the natural operator sequence by shifting the position of the right headpiece by one base-pair step towards the center of O1.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Lactose Operon RepressorC [auth A],
D [auth B],
E [auth C]
333Escherichia coliMutation(s): 0 
Gene Names: lacI
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*T)-3'A [auth D]23N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'B [auth E]23N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPF
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: 4.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 255.771α = 90
b = 255.771β = 90
c = 206.795γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2001-09-04 
  • Released Date: 2001-10-05 
  • Deposition Author(s): Bell, C.E., Lewis, M.

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary