6F7G | pdb_00006f7g

Tryptophan Repressor TrpR from E.coli with 5-Methyltryptamine

• PDB DOI: https://doi.org/10.2210/pdb6F7G/pdb

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


• Deposited: 2017-12-08 Released: 2018-12-19 
• 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: 1.66 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Tryptophan Repressor TrpR: A ligand specificity study

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)

Macromolecule Content 

• Total Structure Weight: 24.02 kDa 
• Atom Count: 1,992 
• Modeled Residue Count: 201 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A, B [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
CVW	C [auth A], D [auth C]	2-(5-methyl-1~{H}-indol-3-yl)ethanamine C11 H14 N2 PYOUAIQXJALPKW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CVW	BindingDB:  6F7G	Kd: 2.88e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.349	α = 90
b = 55.548	β = 98.82
c = 66.992	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-19 
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: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description