6RXB

Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with minocycline

PDB DOI: https://doi.org/10.2210/pdb6RXB/pdb

Classification: TRANSCRIPTION
Organism(s): Acinetobacter baumannii AYE
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-06-07 Released: 2020-07-15
Deposition Author(s): Tam, H.K., Himpich, S., Pos, K.M.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.276
R-Value Work: 0.240
R-Value Observed: 0.242

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

Binding of Tetracyclines to Acinetobacter baumannii TetR Involves Two Arginines as Specificity Determinants

Sumyk, M., Himpich, S., Foong, W.E., Herrmann, A., Pos, K.M., Tam, H.K.

(2021) Front Microbiol

DOI: https://doi.org/10.3389/fmicb.2021.711158

Macromolecule Content

Total Structure Weight: 99 kDa
Atom Count: 6,219
Modelled Residue Count: 747
Deposited Residue Count: 856
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetracycline repressor protein class G	A [auth B], B [auth D]	214	Acinetobacter baumannii AYE	Mutation(s): 1 Gene Names: tetR, ABAYE3639
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetracycline repressor protein class G	C [auth A], D [auth C]	214	Acinetobacter baumannii AYE	Mutation(s): 1 Gene Names: tetR, ABAYE3639
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MIY (Subject of Investigation/LOI) Query on MIY Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth D] SDF format, chain K [auth A] SDF format, chain O [auth C] MOL2 format, chain E [auth B] MOL2 format, chain G [auth D] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] mmCIF format, chain E [auth B] mmCIF format, chain G [auth D] mmCIF format, chain K [auth A] mmCIF format, chain O [auth C]	E [auth B], G [auth D], K [auth A], O [auth C]	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE C₂₃ H₂₇ N₃ O₇ DYKFCLLONBREIL-KVUCHLLUSA-N		Interactions Focus chain E [auth B] Focus chain G [auth D] Focus chain K [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth B] Focus chain G [auth D] Focus chain K [auth A] Focus chain O [auth C]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain N [auth A] MOL2 format, chain I [auth D] MOL2 format, chain N [auth A] mmCIF format, chain I [auth D] mmCIF format, chain N [auth A]	I [auth D], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth D] Focus chain N [auth A] Interactions & Density Focus chain I [auth D] Focus chain N [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain L [auth A] SDF format, chain P [auth C] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain L [auth A] MOL2 format, chain P [auth C] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain L [auth A] mmCIF format, chain P [auth C]	F [auth B], H [auth D], L [auth A], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Focus chain L [auth A] Focus chain P [auth C] Interactions & Density Focus chain F [auth B] Focus chain H [auth D] Focus chain L [auth A] Focus chain P [auth C]