7VMY

Crystal structure of LimF prenyltransferase bound with GSPP


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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GST (Subject of Investigation/LOI)
Query on GST

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
GERANYL S-THIOLODIPHOSPHATE
C10 H20 O6 P2 S
AKIXWSDUEPPMKM-JXMROGBWSA-N
BTB (Subject of Investigation/LOI)
Query on BTB

Download Ideal Coordinates CCD File 
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)
Query on MG

Download Ideal Coordinates CCD File 
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 = 47.28α = 100.124
b = 47.52β = 104.693
c = 61.19γ = 96.679
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata 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