2JHE | pdb_00002jhe

N-terminal domain of TyrR transcription factor (residues 1 - 190)

• PDB DOI: https://doi.org/10.2210/pdb2JHE/pdb

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


• Deposited: 2007-02-21 Released: 2008-06-24 
• Deposition Author(s): Verger, D., Carr, P.D., Kwok, T., Ollis, D.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.317 (Depositor) 
• R-Value Work: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Crystal Structure of the N-Terminal Domain of the Tyrr Transcription Factor Responsible for Gene Regulation of Aromatic Amino Acid Biosynthesis and Transport in Escherichia Coli K12

Verger, D., Carr, P.D., Kwok, T., Ollis, D.L.

(2007) J Mol Biol 367: 102

• PubMed: 17222426 
• DOI: https://doi.org/10.1016/j.jmb.2006.12.018
• Primary Citation Related Structures: 
  2JHE


• PubMed Abstract: 
  

  The X-ray structure of the N-terminal domain of TyrR has been solved to a resolution of 2.3 A. It reveals a modular protein containing an ACT domain, a connecting helix, a PAS domain and a C-terminal helix. Two dimers are present in the asymmetric unit with one monomer of each pair exhibiting a large rigid-body movement that results in a hinging around residue 74 of approximately 50 degrees . The structure of the dimer is discussed with reference to other transcription regulator proteins. Putative binding sites are identified for the aromatic amino acid cofactors.

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Organizational Affiliation: 
• School of Crystallography, Birkbeck College, University of London, UK.

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 PQS (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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 87.51 kDa 
• Atom Count: 5,900 
• Modeled Residue Count: 754 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION REGULATOR TYRR	A, B, C, D	190	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P07604 (Escherichia coli (strain K12)) Explore P07604  Go to UniProtKB:  P07604

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A], H [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
AE3	E [auth A]	2-(2-ETHOXYETHOXY)ETHANOL C6 H14 O3 XXJWXESWEXIICW-UHFFFAOYSA-N
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.317 (Depositor) 
• R-Value Work:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.456	α = 90
b = 72.009	β = 98.46
c = 96.814	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Verger, D., Carr, P.D., Kwok, T., Ollis, D.L.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Source and taxonomy
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other