6EJZ

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

PDB DOI: https://doi.org/10.2210/pdb6EJZ/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli 55989
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-09-24 Released: 2019-02-06
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: 1.90 Å
R-Value Free: 0.218
R-Value Work: 0.184
R-Value Observed: 0.186

Starting Model: experimental
View more details

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: 55.79 kDa
Atom Count: 3,675
Modelled Residue Count: 408
Deposited Residue Count: 464
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, C, D	116	Escherichia coli 55989	Mutation(s): 0 Gene Names: trpR, EC55989_5055
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IAC Query on IAC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth D]	E [auth A], I [auth B], M [auth C], R [auth D], V [auth D]	1H-INDOL-3-YLACETIC ACID C₁₀ H₉ N O₂ SEOVTRFCIGRIMH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], S [auth D], T [auth D], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.44	α = 90
b = 82.44	β = 90
c = 75.65	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-02-06

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: 2019-02-06
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