3F0D	Lyase	date	Oct 24, 2008
title	High Resolution Crystal Structure Of 2c-Methyl-D-Erythritol Cyclodiphosphatase Synthase From Burkholderia Pseudomallei
authors	Seattle Structural Genomics Center For Infectious Disease (S
compound		source
Molecule: 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synt Chain: A, B, C, D, E, F Synonym: Mecps, Mecdp-Synthase Ec: 4.6.1.12 Engineered: Yes		Organism_scientific: Burkholderia Pseudomallei Organism_common: Pseudomonas Pseudomallei Organism_taxid: 28450 Strain: 1710b Gene: Ispf, Mecs, Bpsl2098 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ava0421
symmetry	Space Group: C 1 2 1	R_factor 0.185 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 157.887 69.042 116.581 90.00 130.15 90.00
method	X-Ray Diffraction	resolution	1.20 Å
ligand	ZN	enzyme	Lyase E.C.4.6.1.12 BRENDA
note	3F0D is a representative structure
Gene Ontology	Chain Function Process Component F, A, D, C, E, B
Primary reference	Combining functional and structural genomics to sample the essential Burkholderia structome., Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D 3rd, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC, PLoS One. 2013;8(1):e53851. doi: 10.1371/journal.pone.0053851. Epub 2013 Jan 31. PMID:23382856

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (294 Kb) [Save to disk] Biological Unit Coordinates (3f0d.pdb1.gz) 145 Kb Biological Unit Coordinates (3f0d.pdb2.gz) 145 Kb LPC: Ligand-Protein Contacts for 3F0D CSU: Contacts of Structural Units for 3F0D Likely Quarternary Molecular Structure file(s) for 3F0D Structure Factors (3909 Kb) Retrieve 3F0D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3F0D from S2C, [Save to disk] Re-refined 3f0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3F0D 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 3F0D

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 3F0D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3f0d] [3f0d_D] [3f0d_E] [3f0d_F] [3f0d_B] [3f0d_A] [3f0d_C] SWISS-PROT database: [Q63T71] Domain organization of [ISPF_BURPS] by SWISSPFAM

Other resources with information on 3F0D

Community annotation for 3F0D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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