2PMP	Lyase	date	Apr 23, 2007
title	Structure Of 2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate Syn The Isoprenoid Biosynthetic Pathway Of Arabidopsis Thaliana
authors	B.M.Calisto, J.Perez-Gil, J.Querol-Audi, I.Fita, S.Imperial
compound		source
Molecule: 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synt Chain: A Fragment: Ispf Synonym: Mecps, Mecdp-Synthase Ec: 4.6.1.12 Engineered: Yes		Organism_scientific: Arabidopsis Thaliana Organism_common: Thale Cress Organism_taxid: 3702 Strain: Ecotype Columbia 0 Gene: Ispf Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 (De3) [Plyss] Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet23b
symmetry	Space Group: I 41 3 2	R_factor 0.198 R_Free 0.251
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.795 135.795 135.795 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	C5P, CL, PO4, ZN	enzyme	Lyase E.C.4.6.1.12 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Biosynthesis of isoprenoids in plants: Structure of the 2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana. Comparison with the bacterial enzymes., Calisto BM, Perez-Gil J, Bergua M, Querol-Audi J, Fita I, Imperial S, Protein Sci. 2007 Sep;16(9):2082-8. Epub 2007 Jul 27. PMID:17660251

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk] Biological Unit Coordinates (2pmp.pdb1.gz) 78 Kb LPC: Ligand-Protein Contacts for 2PMP CSU: Contacts of Structural Units for 2PMP Likely Quarternary Molecular Structure file(s) for 2PMP Structure Factors (78 Kb) Retrieve 2PMP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PMP from S2C, [Save to disk] Re-refined 2pmp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2PMP 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 2PMP

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 2PMP, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2pmp_A] [2pmp] SWISS-PROT database: [Q9CAK8] Domain organization of [ISPF_ARATH] by SWISSPFAM

Other resources with information on 2PMP

Community annotation for 2PMP at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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