3D4J	Lyase	date	May 14, 2008
title	Crystal Structure Of Human Mevalonate Diphosphate Decarboxyl
authors	N.E.Voynova, Z.Fu, K.Battaile, T.J.Herdendorf, J.J.P.Kim, H.M.Mi
compound		source
Molecule: Diphosphomevalonate Decarboxylase Chain: A, B Synonym: Mevalonate Pyrophosphate Decarboxylase, Mevalonate (Diphospho)Decarboxylase; Ec: 4.1.1.33 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Man Organism_taxid: 9606 Gene: Mvd, Mpd Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-3d
symmetry	Space Group: P 1 21 1	R_factor 0.218 R_Free 0.274
crystal cell	length a length b length c angle alpha angle beta angle gamma 86.960 53.190 97.790 90.00 107.25 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	SO4	enzyme	Lyase E.C.4.1.1.33 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure., Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM, Arch Biochem Biophys. 2008 Dec 1;480(1):58-67. Epub 2008 Sep 18. PMID:18823933

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (120 Kb) [Save to disk] Biological Unit Coordinates (3d4j.pdb1.gz) 115 Kb LPC: Ligand-Protein Contacts for 3D4J CSU: Contacts of Structural Units for 3D4J Likely Quarternary Molecular Structure file(s) for 3D4J Structure Factors (265 Kb) Retrieve 3D4J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3D4J from S2C, [Save to disk] Re-refined 3d4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D4J 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 3D4J

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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 3D4J, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d4j_A] [3d4j] [3d4j_B] SWISS-PROT database: [P53602] Domain organization of [ERG19_HUMAN] by SWISSPFAM

Other resources with information on 3D4J

Community annotation for 3D4J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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