4PFA | pdb_00004pfa

Crystal structure of M. tuberculosis in complex with BTO - covalent adduct

• PDB DOI: https://doi.org/10.2210/pdb4PFA/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-28 Released: 2015-10-21 
• Deposition Author(s): Neres, J., Panda, M., Cole, S.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.307 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Literature

Crystal structure of M. tuberculosis in complex with BTO

Neres, J., Cole, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.86 kDa 
• Atom Count: 6,672 
• Modeled Residue Count: 843 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable decaprenylphosphoryl-beta-D-ribose oxidase	A, B	480	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dprE1, Rv3790 EC: 1 (PDB Primary Data), 1.1.98.3 (UniProt)
UniProt
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJF1  Go to UniProtKB:  P9WJF1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
N77	D [auth A], F [auth B]	7-(hydroxyamino)-N-(pyridin-3-ylmethyl)-5-(trifluoromethyl)-1,3-benzothiazole-2-carboxamide 3-oxide C15 H11 F3 N4 O3 S GENRUIYZXCGKPM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.307 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.856	α = 90
b = 82.013	β = 100.77
c = 81.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Neres, J., Panda, M., Cole, S.

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Funding Organization	Location	Grant Number
European Commission	Switzerland	MM4TB - 260872

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references
• Version 1.3: 2024-10-16
  Changes: Structure summary