3EDC | pdb_00003edc

Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli Lac-repressor Refined to 2.1 Resolution

• PDB DOI: https://doi.org/10.2210/pdb3EDC/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-03 Released: 2008-11-25 
• Deposition Author(s): Stenberg, K.A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.201 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.156 (Depositor) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a 1.6-hexanediol bound tetrameric form of Escherichia coli lac-repressor refined to 2.1 A resolution

Stenberg, K.A.E., Vihinen, M.

(2009) Proteins 75: 748-759

• PubMed: 19004002 
• DOI: https://doi.org/10.1002/prot.22284
• Primary Citation Related Structures: 
  3EDC


• PubMed Abstract: 
  

  We report the structure of a novel tetrameric form of the lactose repressor (LacI) protein from Escherichia coli refined to 2.1 A resolution. The tetramer is bound to 1.6-hexanediol present in the crystallization solution and the final R(free) for the structure is 0.201. The structure confirms previously reported structures on the monomer level. However, the tetramer is much more densely packed. This adds a new level of complexity to the interpretation of mutational effects and challenges details in the current model for LacI function. Several amino acids, previously associated with changes in function but unexplained at the structural level, appear in a new structural context in this tetramer which provides new implications for their function.

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Organizational Affiliation: 
• Faculty of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 154.98 kDa 
• Atom Count: 9,549 
• Modeled Residue Count: 1,200 
• Deposited Residue Count: 1,440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose operon repressor	A, B, C, D	360	Escherichia coli K-12	Mutation(s): 0
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
HEZ	E [auth A], F [auth B], G [auth C], H [auth D]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.201 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.156 (Depositor) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.15	α = 90
b = 72.434	β = 113.96
c = 130.566	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Stenberg, K.A.E.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description