3AFI	Hydrolase	date	Mar 02, 2010
title	Crystal Structure Of Dbja (His-Dbja)
authors	Y.Sato, T.Senda
compound		source
Molecule: Haloalkane Dehalogenase Chain: E, A, B, F Ec: 3.8.1.5 Engineered: Yes		Organism_scientific: Bradyrhizobium Japonicum Organism_taxid: 224911 Strain: Usda 110 Gene: Dbja Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pybja2
symmetry	Space Group: P 21 21 2	R_factor 0.167 R_Free 0.191
crystal cell	length a length b length c angle alpha angle beta angle gamma 212.855 117.843 55.796 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.75 Å
ligand	CL	enzyme	Hydrolase E.C.3.8.1.5 BRENDA
Gene Ontology	Chain Function Process Component F, A, E, B
Primary reference	Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering., Prokop Z, Sato Y, Brezovsky J, Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, van Leeuwen JG, Janssen DB, Florian J, Nagata Y, Senda T, Damborsky J, Angew Chem Int Ed Engl. 2010 Aug 16;49(35):6111-5. PMID:20645368

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk] Biological Unit Coordinates (3afi.pdb1.gz) 104 Kb Biological Unit Coordinates (3afi.pdb2.gz) 105 Kb LPC: Ligand-Protein Contacts for 3AFI CSU: Contacts of Structural Units for 3AFI Structure Factors (3042 Kb) Retrieve 3AFI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3AFI from S2C, [Save to disk] Re-refined 3afi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3AFI 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 3AFI

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 3AFI, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3afi_F] [3afi] [3afi_E] [3afi_A] [3afi_B] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3AFI

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

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