4UTK | pdb_00004utk

XenA - reduced - Y183F variant

• PDB DOI: https://doi.org/10.2210/pdb4UTK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-07-21 Released: 2015-08-05 
• Deposition Author(s): Werther, T., Dobbek, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

Werther, T., Wahlefeld, S., Salewski, J., Kuhlmann, U., Zebger, I., Hildebrandt, P., Dobbek, H.

(2017) Nat Commun 8: 16084

• DOI: https://doi.org/10.1038/ncomms16084

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 40.84 kDa 
• Atom Count: 3,356 
• Modeled Residue Count: 359 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XENOBIOTIC REDUCTASE	A	365	Pseudomonas putida	Mutation(s): 1  EC: 1.6.99.1
UniProt
Find proteins for Q3ZDM6 (Pseudomonas putida) Explore Q3ZDM6  Go to UniProtKB:  Q3ZDM6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNR	B [auth A]	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL C17 H23 N4 O9 P YTNIXZGTHTVJBW-SCRDCRAPSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.67	α = 90
b = 83.45	β = 90
c = 157.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Werther, T., Dobbek, H.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 2.0: 2017-08-16
  Changes: Atomic model, Database references
• Version 2.1: 2017-09-13
  Changes: Database references
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description