6M8V | pdb_00006m8v

Crystal structure of UbiX-like FMN prenyltransferase MJ0101 from Methanocaldococcus jannaschii, FMN complex

• PDB DOI: https://doi.org/10.2210/pdb6M8V/pdb

• Classification: LYASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-22 Released: 2020-02-26 
• Deposition Author(s): Stogios, P.J., Skarina, T., Khusnutdinova, 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: 2.22 Å
• R-Value Free: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UbiX-like FMN prenyltransferase MJ0101 from Methanocaldococcus jannaschii, 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: 21.5 kDa 
• Atom Count: 1,598 
• Modeled Residue Count: 183 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin prenyltransferase UbiX	A	184	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: ubiX, MJ0102 EC: 2.5.1.129
UniProt
Find proteins for Q57566 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57566  Go to UniProtKB:  Q57566

Small Molecules

Ligands 3 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
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.44	α = 90
b = 133.44	β = 90
c = 133.44	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., Khusnutdinova, 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