6M8T

Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, FMN complex

• PDB DOI: https://doi.org/10.2210/pdb6M8T/pdb

• Classification: LYASE
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-22 Released: 2020-02-26 
• Deposition Author(s): Stogios, P.J., Skarina, T., Khusnutidnova, A., Wawrzak, Z., Yakunin, A.F., Savchenko, A.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.174 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Starting Model: experimental

Literature

Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, FMN complex

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 21.4 kDa 
• Atom Count: 1,727 
• Modelled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin prenyltransferase UbiX	A	189	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0  Gene Names: ubiX, AF_1214 EC: 2.5.1.129
UniProt
Find proteins for O29054 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29054  Go to UniProtKB:  O29054

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.174 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.56	α = 90
b = 98.56	β = 90
c = 98.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Stogios, P.J., Skarina, T., Khusnutidnova, A., Wawrzak, Z., Yakunin, A.F., Savchenko, A.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description