6EKP

Tryptophan Repressor TrpR from E.coli variant T44L T81M S88Y with Indole-3-acetic acid as ligand

PDB DOI: https://doi.org/10.2210/pdb6EKP/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2017-09-26 Released: 2019-01-30
Deposition Author(s): Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.190
R-Value Work: 0.172
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A biosensor for the direct visualization of auxin

Herud-Sikimic, O., Stiel, A.C., Kolb, M., Shanmugaratnam, S., Berendzen, K.W., Feldhaus, C., Hocker, B., Juergens, G.

(2021) Nature

DOI: https://doi.org/10.1038/s41586-021-03425-2

Macromolecule Content

Total Structure Weight: 27.72 kDa
Atom Count: 1,980
Modelled Residue Count: 206
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A, B	116	Escherichia coli K-12	Mutation(s): 3 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P3G Query on P3G Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	3,6,9,12,15-PENTAOXAHEPTADECANE C₁₂ H₂₆ O₅ HYDWALOBQJFOMS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IAC Query on IAC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	1H-INDOL-3-YLACETIC ACID C₁₀ H₉ N O₂ SEOVTRFCIGRIMH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.190
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.035	α = 90
b = 63.123	β = 90
c = 64.64	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(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: 2021-04-07
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description

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Help and Resources

6EKP

Tryptophan Repressor TrpR from E.coli variant T44L T81M S88Y with Indole-3-acetic acid as ligand

A biosensor for the direct visualization of auxin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)