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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.276 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

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

Walkiewicz, K., Shamoo, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A], L [auth B], P [auth C], T [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MIY	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
SO4	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.276 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.219 (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

Entry History 

Deposition Data

• Released Date: 2013-01-02 
Deposition Author(s): Walkiewicz, K., Shamoo, Y.

Revision History  

• 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