3V3N | pdb_00003v3n

Crystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline

PDB DOI: https://doi.org/10.2210/pdb3V3N/pdb

Classification: OXIDOREDUCTASE/ANTIBIOTIC
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-12-13 Released: 2013-01-02
Deposition Author(s): Walkiewicz, K., Shamoo, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.276 (Depositor), 0.270 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

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

Crystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline

Walkiewicz, K., Shamoo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 175.75 kDa
Atom Count: 12,093
Modelled Residue Count: 1,470
Deposited Residue Count: 1,512
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetX2 protein	A, B, C, D	378	Bacteroides thetaiotaomicron	Mutation(s): 3 Gene Names: tetX2 EC: 1.14.13.231
UniProt
Find proteins for Q93L51 (Bacteroides thetaiotaomicron) Explore Q93L51 Go to UniProtKB: Q93L51
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93L51
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], P [auth C], T [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
MIY Query on MIY 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 Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], I [auth B], M [auth C], Q [auth D]	(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 A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	F [auth A] G [auth A] J [auth B] K [auth B] N [auth C] F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.276 (Depositor), 0.270 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.426	α = 111.11
b = 80.102	β = 90.1
c = 87.362	γ = 93.01

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-02

Deposition Author(s):

Walkiewicz, K.

Shamoo, Y.

Revision History (Full details and data files)

Version 1.0: 2013-01-02
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary