6FAL | pdb_00006fal

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

PDB DOI: https://doi.org/10.2210/pdb6FAL/pdb

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

Deposited: 2017-12-15 Released: 2019-01-30
Deposition Author(s): Stiel, A.C., Shanmugaratnam, S., Hocker, B.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.179 (Depositor), 0.180 (DCC)
R-Value Work:
0.162 (Depositor), 0.170 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Tryptophan Repressor TrpR from E.coli: A ligand binding study

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

To be published.

Macromolecule Content

Total Structure Weight: 27.15 kDa
Atom Count: 1,869
Modeled Residue Count: 194
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A, B	115	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOP Query on IOP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	INDOLYLPROPIONIC ACID C₁₁ H₁₁ N O₂ GOLXRNDWAUTYKT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.179 (Depositor), 0.180 (DCC)
R-Value Work: 0.162 (Depositor), 0.170 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.07	α = 90
b = 45.25	β = 104.02
c = 60.67	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Shanmugaratnam, S.

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

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2019-12-25
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.