6ECF Hydrolase date Aug 07, 2018
title Vlm2 Thioesterase Domain With Genetically Encoded 2,3-Diamin Acid Bound With A Dodecadepsipeptide, Space Group P1
authors D.A.Alonzo, N.Huguenin-Dezot, G.W.Heberlig, M.Mahesh, D.P.Nguyen M.H.Dornan, C.N.Boddy, J.W.Chin, T.M.Schmeing
compound source
Molecule: Vlm2
Chain: A, B, C, D, E, F
Fragment: Thioesterase Domain (Unp Residues 2368-2655)
Ec: 3.1.2.-
Engineered: Yes
Organism_scientific: Streptomyces Tsusimaensis
Organism_taxid: 285482
Atcc: 15141
Gene: Vlm2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dodecadepsipeptide
Chain: G, I, H, K, J, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.197 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.996 77.129 90.329 91.77 114.89 117.94
method X-Ray Diffractionresolution 2.50 Å
ligand 2OP, DPP, DVA, VAD enzyme Hydrolase E.C.3.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceTrapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid., Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW, Nature. 2018 Dec 12. pii: 10.1038/s41586-018-0781-z. doi:, 10.1038/s41586-018-0781-z. PMID:30542153
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (445 Kb) [Save to disk]
  • Biological Unit Coordinates (6ecf.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (6ecf.pdb2.gz) 76 Kb
  • Biological Unit Coordinates (6ecf.pdb3.gz) 76 Kb
  • Biological Unit Coordinates (6ecf.pdb4.gz) 78 Kb
  • Biological Unit Coordinates (6ecf.pdb5.gz) 76 Kb
  • Biological Unit Coordinates (6ecf.pdb6.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 6ECF
  • CSU: Contacts of Structural Units for 6ECF
  • Structure Factors (2013 Kb)
  • Retrieve 6ECF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ECF from S2C, [Save to disk]
  • View 6ECF in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6ECF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ecf_D] [6ecf_E] [6ecf_H] [6ecf_C] [6ecf_L] [6ecf_F] [6ecf_I] [6ecf_B] [6ecf_A] [6ecf_J] [6ecf_G] [6ecf_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6ECF
  • Community annotation for 6ECF at PDBWiki (http://pdbwiki.org)

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