6M8U | pdb_00006m8u

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

• PDB DOI: https://doi.org/10.2210/pdb6M8U/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., Khusnutidinova, A., Wawrzak, Z., Yakunin, A.F., Savchenko, A.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, prenylated-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: 21.47 kDa 
• Atom Count: 1,582 
• Modeled Residue Count: 183 
• 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
4LU	B [auth A]	1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol C22 H30 N4 O9 P KOUJZPGFPGLHCZ-IYOUNJFTSA-O
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.72	α = 90
b = 98.72	β = 90
c = 98.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	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., Khusnutidinova, A., Wawrzak, Z., Yakunin, A.F., Savchenko, A.

---

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, Derived calculations, Refinement description, Structure summary