2DDT	Hydrolase	date	Feb 02, 2006
title	Crystal Structure Of Sphingomyelinase From Bacillus Cereus W Magnesium Ion
authors	H.Ago, M.Oda, H.Tsuge, N.Katunuma, M.Miyano, J.Sakurai, Riken Stru Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Sphingomyelin Phosphodiesterase Chain: A, B Synonym: Sphingomyelinase Ec: 3.1.4.12 Engineered: Yes		Organism_scientific: Bacillus Cereus Organism_taxid: 1396 Strain: Iam 1029 Expression_system: Bacillus Subtilis Expression_system_taxid: 1423 Expression_system_strain: Isw1214 Expression_system_vector_type: Plasmid Expression_system_plasmid: Phy300plk
symmetry	Space Group: P 1	R_factor 0.193 R_Free 0.230
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.844 50.893 59.506 81.87 81.84 79.68
method	X-Ray Diffraction	resolution	1.80 Å
ligand	MES, MG, SO4	enzyme	Hydrolase E.C.3.1.4.12 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from bacillus cereus., Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J, J Biol Chem. 2006 Apr 4;. PMID:16595670

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk] Biological Unit Coordinates (2ddt.pdb1.gz) 52 Kb Biological Unit Coordinates (2ddt.pdb2.gz) 52 Kb LPC: Ligand-Protein Contacts for 2DDT CSU: Contacts of Structural Units for 2DDT Likely Quarternary Molecular Structure file(s) for 2DDT Structure Factors (379 Kb) Retrieve 2DDT in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DDT from S2C, [Save to disk] Re-refined 2ddt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DDT 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 2DDT

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 2DDT, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ddt_A] [2ddt] [2ddt_B] SWISS-PROT database: [P11889] Domain organization of [PHL2_BACCE] by SWISSPFAM

Other resources with information on 2DDT

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

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