4AB4

Structure of Xenobiotic Reductase B from Pseudomonas putida in complex with TNT

• PDB DOI: https://doi.org/10.2210/pdb4AB4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida KT2440
• Mutation(s): No 


• Deposited: 2011-12-06 Released: 2012-12-19 
• Deposition Author(s): Carvalho, A.L., Mukhopadhyay, A., Romao, M.J., Bursakov, S., Kladova, A., Ramos, J.L., van Dillewijn, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.184 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Structural Determinants of Aromatic Ring Reduction in the Xenobiotic Reductase B from Pseudomonas Putida

Carvalho, A.L., Mukhopadhyay, A., Bonifacio, C., Romao, M.J., Bursakov, S., Kladova, A., Ramos, J.L., Van Dillewijn, P.

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)

Macromolecule Content

• Total Structure Weight: 80.74 kDa 
• Atom Count: 6,286 
• Modelled Residue Count: 698 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XENOBIOTIC REDUCTASE B	A, B	362	Pseudomonas putida KT2440	Mutation(s): 0
UniProt
Find proteins for Q88PD0 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88PD0  Go to UniProtKB:  Q88PD0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
TNL	I [auth A], M [auth B]	2,4,6-TRINITROTOLUENE C7 H5 N3 O6 SPSSULHKWOKEEL-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.184 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.01	α = 90
b = 104.87	β = 90
c = 106.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Carvalho, A.L., Mukhopadhyay, A., Romao, M.J., Bursakov, S., Kladova, A., Ramos, J.L., van Dillewijn, P.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description