2PAQ	Hydrolase	date	Mar 27, 2007
title	Crystal Structure Of The 5'-Deoxynucleotidase Yfbr
authors	M.D.Zimmerman, M.Chruszcz, M.Cymborowski, M.Kudritska, W.Minor, M Center For Structural Genomics (Mcsg)
compound		source
Molecule: 5'-Deoxynucleotidase Yfbr Chain: A, B Synonym: Nucleoside 5'-Monophosphate Phosphohydrolase, 5'- Deoxyribonucleotidase; Ec: 3.1.3.5 Engineered: 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: B834(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Modified Pet-15b
symmetry	Space Group: H 3	R_factor 0.187 R_Free 0.237
crystal cell	length a length b length c angle alpha angle beta angle gamma 137.023 137.023 56.288 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	MSE	enzyme	Hydrolase E.C.3.1.3.5 BRENDA
note	2PAQ supersedes 1WPH
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] (69 Kb) [Save to disk] Biological Unit Coordinates (2paq.pdb1.gz) 59 Kb Biological Unit Coordinates (2paq.pdb2.gz) 172 Kb LPC: Ligand-Protein Contacts for 2PAQ CSU: Contacts of Structural Units for 2PAQ Likely Quarternary Molecular Structure file(s) for 2PAQ Structure Factors (529 Kb) Retrieve 2PAQ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PAQ from S2C, [Save to disk] Re-refined 2paq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2PAQ 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 2PAQ

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 2PAQ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2paq] [2paq_A] [2paq_B] SWISS-PROT database: [P76491] Domain organization of [YFBR_ECOLI] by SWISSPFAM Domain found in 2PAQ: [HDc ] by SMART

Other resources with information on 2PAQ

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

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