2PE5

Crystal Structure of the Lac Repressor bound to ONPG in repressed state

• PDB DOI: https://doi.org/10.2210/pdb2PE5/pdb
• NAKB: 2PE5

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-04-02 Released: 2008-03-18 
• Deposition Author(s): Daber, R., Stayrook, S.E., Rosenberg, A., Lewis, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.287 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 125.53 kDa 
• Atom Count: 8,527 
• Modelled Residue Count: 1,037 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose operon repressor	D [auth A], E [auth B], F [auth C]	330	Escherichia coli	Mutation(s): 1  Gene Names: lacI
UniProt
Find proteins for P03023 (Escherichia coli (strain K12)) Explore P03023  Go to UniProtKB:  P03023

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')	A [auth D], B [auth E], C [auth F]	20	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
145	G [auth A], H [auth B], I [auth C]	2-nitrophenyl beta-D-galactopyranoside C12 H15 N O8 KUWPCJHYPSUOFW-YBXAARCKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.287 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 253.08	α = 90
b = 253.08	β = 90
c = 203.247	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Daber, R., Stayrook, S.E., Rosenberg, A., Lewis, M.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-30
  Changes: Data collection, Refinement description