7VMW

Crystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LynF/TruF/PatF family peptide O-prenyltransferase
A, B
302Limnothrix sp. CACIAM 69dMutation(s): 0 
Gene Names: BJG00_018450
UniProt
Find proteins for A0A372DCN7 (Limnothrix sp. CACIAM 69d)
Explore A0A372DCN7 
Go to UniProtKB:  A0A372DCN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A372DCN7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
substrate peptide7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.66α = 90
b = 48.43β = 117.869
c = 91.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-10-09
    Changes: Structure summary