6ECF

Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group P1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.

Huguenin-Dezot, N.Alonzo, D.A.Heberlig, G.W.Mahesh, M.Nguyen, D.P.Dornan, M.H.Boddy, C.N.Schmeing, T.M.Chin, J.W.

(2019) Nature 565: 112-117


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vlm2
A, B, C, D, E, F
303Streptomyces tsusimaensisMutation(s): 0 
Gene Names: vlm2
Find proteins for Q1PSF3 (Streptomyces tsusimaensis)
Go to UniProtKB:  Q1PSF3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
dodecadepsipeptide
G, I, H, K, J, L
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
DVA
Query on DVA
G, H, I, J, K, L
D-PEPTIDE LINKINGC5 H11 N O2

--

2OP
Query on 2OP
G, H, I, J, K, L
NON-POLYMERC3 H6 O3

--

VAD
Query on VAD
G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H10 O3VAL
DPP
Query on DPP
A, B, C, D, E, F
L-PEPTIDE LINKINGC3 H8 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 76.996α = 91.77
b = 77.129β = 114.89
c = 90.329γ = 117.94
Software Package:
Software NamePurpose
Aimlessdata scaling
DIALSdata reduction
PHENIXrefinement
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada106615

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references