6YR2 | pdb_00006yr2

TetR(D) soaked with Tigecycline P4(1)2(1)2

PDB DOI: https://doi.org/10.2210/pdb6YR2/pdb

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

Deposited: 2020-04-19 Released: 2021-04-28
Deposition Author(s): Hinrichs, W., Stary, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.210 (Depositor), 0.220 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

TetR(D) soaked with Tigecycline

Hinrichs, W., Stary, K.

To be published.

Macromolecule Content

Total Structure Weight: 47.66 kDa
Atom Count: 3,436
Modeled Residue Count: 404
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetracycline repressor protein class D	A [auth AAA], B [auth BBB]	207	Escherichia coli	Mutation(s): 1 Gene Names: tetR
UniProt
Find proteins for P0ACT4 (Escherichia coli) Explore P0ACT4 Go to UniProtKB: P0ACT4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ACT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T1C (Subject of Investigation/LOI) Query on T1C Download Ideal Coordinates CCD File SDF format, chain H [auth BBB] MOL2 format, chain H [auth BBB] mmCIF format, chain H [auth BBB]	H [auth BBB]	TIGECYCLINE C₂₉ H₄₁ N₅ O₈ FPZLLRFZJZRHSY-HJYUBDRYSA-P		Interactions Focus chain H [auth BBB] Interactions & Density Focus chain H [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain J [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain J [auth BBB]	C [auth AAA], J [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain J [auth BBB]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain K [auth BBB] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain G [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain K [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain G [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain K [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain G [auth AAA]	D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] K [auth BBB] D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], K [auth BBB], L [auth BBB], M [auth BBB], N [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth BBB] MOL2 format, chain I [auth BBB] mmCIF format, chain I [auth BBB]	I [auth BBB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth BBB] Interactions & Density Focus chain I [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.210 (Depositor), 0.220 (DCC)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.339	α = 90
b = 68.339	β = 90
c = 178.397	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Hinrichs, W.

Stary, K.

Revision History (Full details and data files)

Version 1.0: 2021-04-28
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description