2Y0F Oxidoreductase date Dec 02, 2010
title Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
authors I.Rekittke, T.Nonaka, J.Wiesner, U.Demmer, E.Warkentin, H.Jomaa, U
compound source
Molecule: 4-Hydroxy-3-Methylbut-2-En-1-Yl Diphosphate Synth
Chain: A, B, C, D
Synonym: 1-Hydroxy-2-Methyl-2-(E)-Butenyl 4-Diphosphate Syn Gcpe;
Ec: 1.17.7.1
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27
Atcc: Baa-163
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Top10
Expression_system_plasmid: Pqettgcpe
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.500 130.970 101.260 90.00 102.10 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand SF4 enzyme Oxidoreductase E.C.1.17.7.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure of the E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate synthase (GcpE) from Thermus thermophilus., Rekittke I, Nonaka T, Wiesner J, Demmer U, Warkentin E, Jomaa H, Ermler U, FEBS Lett. 2010 Dec 15. PMID:21167158
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (535 Kb) [Save to disk]
  • Biological Unit Coordinates (2y0f.pdb1.gz) 264 Kb
  • Biological Unit Coordinates (2y0f.pdb2.gz) 265 Kb
  • LPC: Ligand-Protein Contacts for 2Y0F
  • CSU: Contacts of Structural Units for 2Y0F
  • Structure Factors (541 Kb)
  • Retrieve 2Y0F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y0F from S2C, [Save to disk]
  • Re-refined 2y0f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • 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 2Y0F
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2Y0F, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y0f_A] [2y0f] [2y0f_D] [2y0f_B] [2y0f_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2Y0F
  • Community annotation for 2Y0F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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