5LNJ

XenA - reduced - Y183F variant in complex with 7-hydroxycoumarin

• PDB DOI: https://doi.org/10.2210/pdb5LNJ/pdb

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


• Deposited: 2016-08-04 Released: 2017-08-16 
• Deposition Author(s): Werther, T., Dobbek, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.145 
• R-Value Work: 0.127 
• R-Value Observed: 0.127 

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: 40.45 kDa 
• Atom Count: 3,537 
• Modelled Residue Count: 360 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:flavin oxidoreductase	A	360	Pseudomonas putida	Mutation(s): 1  Gene Names: O999_23785
UniProt
Find proteins for A0A1X0ZT96 (Pseudomonas putida) Explore A0A1X0ZT96  Go to UniProtKB:  A0A1X0ZT96

Small Molecules

Ligands 3 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
07L	C [auth A]	7-hydroxy-2H-chromen-2-one C9 H6 O3 ORHBXUUXSCNDEV-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.145 
• R-Value Work: 0.127 
• R-Value Observed: 0.127 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.62	α = 90
b = 83.46	β = 90
c = 156.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Werther, T., Dobbek, H.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description