Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.08 kDa 
• Atom Count: 4068 
• Modelled Residue Count: 538 
• Deposited Residue Count: 538 
• Unique protein chains: 1

2PAF

Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state

• PDB DOI: 10.2210/pdb2PAF/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-27 Released: 2007-06-19 
• Deposition Author(s): Daber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.195 
• R-Value Observed: 0.199 

Literature

Structural analysis of lac repressor bound to allosteric effectors.

Daber, R., Stayrook, S., Rosenberg, A., Lewis, M.

(2007) J Mol Biol 370: 609-619

• PubMed: 17543986 
• DOI: 10.1016/j.jmb.2007.04.028
• Primary Citation of Related Structures:  
  2P9H, 2PAF, 2PE5


• PubMed Abstract: 
  

The lac operon is a model system for understanding how effector molecules regulate transcription and are necessary for allosteric transitions. The crystal structures of the lac repressor bound to inducer and anti-inducer molecules provide a model for how these small molecules can modulate repressor function. The structures of the apo repressor and the repressor bound to effector molecules are compared in atomic detail. All effectors examined here bind to the repressor in the same location and are anchored to the repressor through hydrogen bonds to several hydroxyl groups of the sugar ring. Inducer molecules form a more extensive hydrogen-bonding network compared to anti-inducers and neutral effector molecules. The structures of these effector molecules suggest that the O6 hydroxyl on the galactoside is essential for establishing a water-mediated hydrogen bonding network that bridges the N-terminal and C-terminal sub-domains. The altered hydrogen bonding can account in part for the different structural conformations of the repressor, and is vital for the allosteric transition.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, PA 19104-6059, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose operon repressor	A, B	269	Escherichia coli	Mutation(s): 0  Gene Names: lacI
UniProt
Find proteins for P03023 (Escherichia coli (strain K12)) Explore P03023  Go to UniProtKB:  P03023

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPF	C [auth A], D [auth B]	2-nitrophenyl beta-D-fucopyranoside C12 H15 N O7 SWRPIVXPHLYETN-BVWHHUJWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.195 
• R-Value Observed: 0.199 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.541	α = 90
b = 77.541	β = 90
c = 212.456	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-27 
• Released Date: 2007-06-19 
Deposition Author(s): Daber, R.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary