2PAR	Hydrolase	date	Mar 27, 2007
title	Crystal Structure Of The 5'-Deoxynucleotidase Yfbr Mutant E7 Complexed With Co(2+) And Tmp
authors	M.D.Zimmerman, M.Proudfoot, A.Yakunin, W.Minor
compound		source
Molecule: 5'-Deoxynucleotidase Yfbr Chain: A, B Synonym: Nucleoside 5'-Monophosphate Phosphohydrolase, 5'- Deoxyribonucleotidase; Ec: 3.1.3.5 Engineered: Yes Mutation: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K12 Gene: Yfbr, B2291, Jw2288 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta2(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Modified Pet-15b
symmetry	Space Group: H 3	R_factor 0.194 R_Free 0.247
crystal cell	length a length b length c angle alpha angle beta angle gamma 136.136 136.136 55.418 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	CO, PEG, TMP	enzyme	Hydrolase E.C.3.1.3.5 BRENDA
Gene Ontology	Chain Function Process Component A, B 5'-deoxynucleotidase activit... phosphatase activity
Primary reference	Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli., Zimmerman MD, Proudfoot M, Yakunin A, Minor W, J Mol Biol. 2008 Apr 18;378(1):215-26. Epub 2008 Mar 4. PMID:18353368

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk] Biological Unit Coordinates (2par.pdb1.gz) 56 Kb Biological Unit Coordinates (2par.pdb2.gz) 164 Kb LPC: Ligand-Protein Contacts for 2PAR CSU: Contacts of Structural Units for 2PAR Likely Quarternary Molecular Structure file(s) for 2PAR Structure Factors (186 Kb) Retrieve 2PAR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PAR from S2C, [Save to disk] Re-refined 2par structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2PAR 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 2PAR

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 2PAR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2par_A] [2par] [2par_B] SWISS-PROT database: [P76491] Domain organization of [YFBR_ECOLI] by SWISSPFAM Domain found in 2PAR: [HDc ] by SMART

Other resources with information on 2PAR

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

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