1YDO	Lyase	date	Dec 24, 2004
title	Crystal Structure Of The Bacillis Subtilis Hmg-Coa Lyase, No Structural Genomics Target Sr181.
authors	F.Forouhar, M.Hussain, W.Edstrom, S.M.Vorobiev, R.Xiao, M.Ciano, L T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structur Genomics Consortium (Nesg)
compound		source
Molecule: Hmg-Coa Lyase Chain: A, B, C, D Synonym: Hypothetical Protein Bsu18230 Engineered: Yes		Organism_scientific: Bacillus Subtilis Subsp. Subtilis Organism_taxid: 224308 Strain: 168 Gene: Yngg Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)+Magic Expression_system_vector_type: Pet21 Expression_system_plasmid: Bl21
symmetry	Space Group: P 1 21 1	R_factor 0.263 R_Free 0.303
crystal cell	length a length b length c angle alpha angle beta angle gamma 62.693 104.666 97.445 90.00 107.43 90.00
method	X-Ray Diffraction	resolution	2.71 Å
ligand	IOD, MSE	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds., Forouhar F, Hussain M, Farid R, Benach J, Abashidze M, Edstrom WC, Vorobiev SM, Xiao R, Acton TB, Fu Z, Kim JJ, Miziorko HM, Montelione GT, Hunt JF, J Biol Chem. 2006 Mar 17;281(11):7533-45. Epub 2005 Dec 5. PMID:16330546

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (200 Kb) [Save to disk] Biological Unit Coordinates (1ydo.pdb1.gz) 99 Kb Biological Unit Coordinates (1ydo.pdb2.gz) 98 Kb Biological Unit Coordinates (1ydo.pdb3.gz) 193 Kb LPC: Ligand-Protein Contacts for 1YDO CSU: Contacts of Structural Units for 1YDO Likely Quarternary Molecular Structure file(s) for 1YDO Retrieve 1YDO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YDO from S2C, [Save to disk]

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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 1YDO

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1YDO, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ydo_D] [1ydo_C] [1ydo] [1ydo_A] [1ydo_B] SWISS-PROT database: [O34873] Domain organization of [HMGCL_BACSU] by SWISSPFAM

Other resources with information on 1YDO

Community annotation for 1YDO at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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