3F6M Lyase date Nov 06, 2008
title Crystal Structure Of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphos Synthase Ispf From Yersinia Pestis
authors Y.Kim, N.Maltseva, J.Stam, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
compound source
Molecule: 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synt
Chain: A
Synonym: Mecps, Mecdp-Synthase
Ec: 4.6.1.12
Engineered: Yes
Organism_scientific: Yersinia Pestis
Organism_taxid: 214092
Strain: Co92
Gene: Ispf, Y0829, Ypo3360, Yp_0327
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Magic
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg19c
symmetry Space Group: I 21 3
R_factor 0.194 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
146.640 146.640 146.640 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.96 Å
ligand MSE enzyme Lyase E.C.4.6.1.12 BRENDA
Gene YP
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (3f6m.pdb1.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 3F6M
  • CSU: Contacts of Structural Units for 3F6M
  • Likely Quarternary Molecular Structure file(s) for 3F6M
  • Structure Factors (214 Kb)
  • Retrieve 3F6M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F6M from S2C, [Save to disk]
  • Re-refined 3f6m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F6M 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 3F6M
  • 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 3F6M, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f6m_A] [3f6m]
  • SWISS-PROT database: [Q8ZBP7]
  • Domain organization of [ISPF_YERPE] by SWISSPFAM
  • Other resources with information on 3F6M
  • Community annotation for 3F6M 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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