6F7F | pdb_00006f7f

Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid

• PDB DOI: https://doi.org/10.2210/pdb6F7F/pdb

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


• Deposited: 2017-12-08 Released: 2019-03-27 
• Deposition Author(s): Stiel, A.C., Shanmugaratnam, S., Hocker, B.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Tryptophan Repressor TrpR: A study of ligand binding specificity

Stiel, A.C., Shanmugaratnam, S., Hocker, B.

To be published.

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: 48.11 kDa 
• Atom Count: 3,686 
• Modelled Residue Count: 408 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A [auth B], B [auth A], C [auth D], D [auth C]	103	Escherichia coli	Mutation(s): 0  Gene Names: trpR, rtrY, b4393, JW4356
UniProt
Find proteins for P0A881 (Escherichia coli (strain K12)) Explore P0A881  Go to UniProtKB:  P0A881

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOP	E [auth B], F [auth A], G [auth D], H [auth C]	INDOLYLPROPIONIC ACID C11 H11 N O2 GOLXRNDWAUTYKT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.84	α = 90
b = 81.84	β = 90
c = 70.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Stiel, A.C., Shanmugaratnam, S., Hocker, B.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	HO 4022/2-3

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description