3P9U

Crystal structure of TetX2 from Bacteroides thetaiotaomicron with substrate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.282 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Crystal structure of Bacteroides thetaiotaomicron TetX2: a tetracycline degrading monooxygenase at 2.8 A resolution.

Walkiewicz, K.Davlieva, M.Wu, G.Shamoo, Y.

(2011) Proteins 79: 2335-2340

  • DOI: https://doi.org/10.1002/prot.23052
  • Primary Citation of Related Structures:  
    3P9U

  • PubMed Abstract: 

    We have determined the structure of Bacteroides thetaiotaomicron TetX2 at 2.8 Å resolution, and shown that it is a class A flavin dependent oxidoreductase. TetX2 has broad activity against a range of tetracyclines including one of the most recent tetracyclines, tigecycline (Tygacil ® ). Comparison of TetX2 with that of the weakly homologous Pseudomonas fluorescens para-hydroxybenzoate hydroxylase (PHBH) (21% identity) shows substantial differences among residues at the substrate binding site although FAD is positioned in a similar conformation between the two enzymes and is poised to carry out catalysis.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, 6100 Main St. MS-140, Houston, Texas, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TetX2 protein
A, B, C, D
378Bacteroides thetaiotaomicronMutation(s): 2 
Gene Names: tetX2
EC: 1.14.13.231
UniProt
Find proteins for Q93L51 (Bacteroides thetaiotaomicron)
Explore Q93L51 
Go to UniProtKB:  Q93L51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93L51
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.282 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.7α = 90
b = 67.33β = 100.31
c = 153.79γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary