3PVJ | pdb_00003pvj

Crystal structure of the Fe(II)/alpha-ketoglutarate dependent taurine dioxygenase from Pseudomonas putida KT2440

• PDB DOI: https://doi.org/10.2210/pdb3PVJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-07 Released: 2011-12-21 
• Deposition Author(s): Knauer, S.H., Spiegelhauer, O., Schwarzinger, S., Haenzelmann, P., Dobbek, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.191 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Biochemical and structural characterization of the Fe(II)/alpha-ketoglutarate dependent taurine dioxygenase from Pseudomonas putida KT2440

Knauer, S.H., Hartl-Spiegelhauer, O., Schwarzinger, S., Haenzelmann, P., Dobbek, H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 124.61 kDa 
• Atom Count: 10,229 
• Modeled Residue Count: 1,103 
• Deposited Residue Count: 1,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent taurine dioxygenase	A, B, C, D	277	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: PP0230, PP_0230, tauD EC: 1.14.11.17
UniProt
Find proteins for Q88RA3 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88RA3  Go to UniProtKB:  Q88RA3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.191 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.249	α = 90
b = 105.339	β = 90
c = 171.43	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Knauer, S.H., Spiegelhauer, O., Schwarzinger, S., Haenzelmann, P., Dobbek, H.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description