1TD5

Crystal Structure of the Ligand Binding Domain of E. coli IclR.

• PDB DOI: https://doi.org/10.2210/pdb1TD5/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-05-21 Released: 2004-07-13 
• Deposition Author(s): Walker, J.R., Evdokimova, L., Zhang, R.-G., Bochkarev, A., Joachimiak, A., Arrowsmith, C., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.299 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structural Analyses of the Ligand Binding Sites of the IclR family of transcriptional regulators

Walker, J.R., Evdokimova, L., Zhang, R.-G., Bochkarev, A., Arrowsmith, C., Edwards, A., Savchenko, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.87 kDa 
• Atom Count: 5,834 
• Modelled Residue Count: 716 
• Deposited Residue Count: 808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetate operon repressor	A, B, C, D	202	Escherichia coli	Mutation(s): 7  Gene Names: ICLR, B4018
UniProt
Find proteins for P16528 (Escherichia coli (strain K12)) Explore P16528  Go to UniProtKB:  P16528

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.299 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.098	α = 90
b = 82.911	β = 90
c = 157.316	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-13 
Deposition Author(s): Walker, J.R., Evdokimova, L., Zhang, R.-G., Bochkarev, A., Joachimiak, A., Arrowsmith, C., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-09
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary