6F9K | pdb_00006f9k

Tryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan as ligand

PDB DOI: https://doi.org/10.2210/pdb6F9K/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-12-14 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: 1.40 Å
R-Value Free:
0.206 (Depositor), 0.200 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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: 14.7 kDa
Atom Count: 1,021
Modeled Residue Count: 106
Deposited Residue Count: 116
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	116	Escherichia coli K-12	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D0Q Query on D0Q Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain B [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain B [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain B [auth A]	B [auth A], G [auth A], H [auth A], I [auth A]	5-methyl-L-tryptophan C₁₂ H₁₄ N₂ O₂ HUNCSWANZMJLPM-JTQLQIEISA-N		Interactions Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.206 (Depositor), 0.200 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.146	α = 90
b = 53.146	β = 90
c = 90.823	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
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):

Stiel, A.C.

Shanmugaratnam, S.

Hocker, B.

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 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references
Version 2.1: 2024-01-17
Changes: Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 6F9K | pdb_00006f9k

Tryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan as ligand

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations