7VMY

Crystal structure of LimF prenyltransferase bound with GSPP

• PDB DOI: https://doi.org/10.2210/pdb7VMY/pdb

• Classification: TRANSFERASE
• Organism(s): Limnothrix sp. CACIAM 69d
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-09 Released: 2022-08-03 
• Deposition Author(s): Hamada, K., Kobayashi, S., Okada, C., Zhang, Y., Inoue, S., Goto, Y., Suga, H., Ogata, K., Sengoku, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates

Zhang, Y., Hamada, K., Nguyen, D.T., Inoue, S., Satake, M., Kobayashi, S., Okada, C., Ogata, K., Okada, M., Sengoku, T., Goto, Y., Suga, H.

(2022) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-022-00822-2

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.58 kDa 
• Atom Count: 5,228 
• Modelled Residue Count: 589 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LynF/TruF/PatF family peptide O-prenyltransferase	A, B	302	Limnothrix sp. CACIAM 69d	Mutation(s): 0  Gene Names: BJG00_018450
UniProt
Find proteins for A0A372DCN7 (Limnothrix sp. CACIAM 69d) Explore A0A372DCN7  Go to UniProtKB:  A0A372DCN7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GST (Subject of Investigation/LOI)	D [auth A], G [auth B]	GERANYL S-THIOLODIPHOSPHATE C10 H20 O6 P2 S AKIXWSDUEPPMKM-JXMROGBWSA-N
BTB (Subject of Investigation/LOI)	E [auth A], H [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.28	α = 100.124
b = 47.52	β = 104.693
c = 61.19	γ = 96.679

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Hamada, K., Kobayashi, S., Okada, C., Zhang, Y., Inoue, S., Goto, Y., Suga, H., Ogata, K., Sengoku, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2022-08-10
  Changes: Structure summary
• Version 1.2: 2022-08-24
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description