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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.229 (Depositor), 0.231 (DCC)
R-Value Work:
0.172 (Depositor), 0.174 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Tryptophan Repressor TrpR: A study of ligand binding specificity

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

To be published.

Macromolecule Content

Total Structure Weight: 48.11 kDa
Atom Count: 3,686
Modeled Residue Count: 408
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 E [auth B] SDF format, chain F [auth A] SDF format, chain G [auth D] SDF format, chain H [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth D] MOL2 format, chain H [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth D] mmCIF format, chain H [auth C]	E [auth B], F [auth A], G [auth D], H [auth C]	INDOLYLPROPIONIC ACID C₁₁ H₁₁ N O₂ GOLXRNDWAUTYKT-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth A] Focus chain G [auth D] Focus chain H [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth A] Focus chain G [auth D] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.229 (Depositor), 0.231 (DCC)
R-Value Work: 0.172 (Depositor), 0.174 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-27

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.