1JY8 Biosynthetic Protein date Sep 11, 2001
title 2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf)
authors S.Steinbacher, J.Kaiser, J.Wungsintaweekul, S.Hecht, W.Eisenreic S.Gerhardt, A.Bacher, F.Rohdich
compound source
Molecule: 2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synth
Chain: A
Synonym: Mecps
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 21 3
R_factor 0.201 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.630 144.630 144.630 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand C5P, CDI, ZN enzyme
related structures by homologous chain: 1U3L, 1VHA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids., Steinbacher S, Kaiser J, Wungsintaweekul J, Hecht S, Eisenreich W, Gerhardt S, Bacher A, Rohdich F, J Mol Biol 2002 Feb 8;316(1):79-88. PMID:11829504
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (1jy8.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 1JY8
  • CSU: Contacts of Structural Units for 1JY8
  • Likely Quarternary Molecular Structure file(s) for 1JY8
  • Structure Factors (143 Kb)
  • Retrieve 1JY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JY8 from S2C, [Save to disk]
  • Re-refined 1jy8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1JY8 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 1JY8
  • 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 1JY8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jy8a_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1jy8_A] [1jy8]
  • SWISS-PROT database: [P62617]
  • Domain organization of [ISPF_ECOLI] by SWISSPFAM
    • Other resources with information on 1JY8
  • Community annotation for 1JY8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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