3B3V Hydrolase date Oct 22, 2007
title Crystal Structure Of The S228a Mutant Of The Aminopeptidase Vibrio Proteolyticus
authors N.J.Ataie, Q.Q.Hoang, M.P.D.Zahniser, A.Milne, G.A.Petsko, D.Ring
compound source
Molecule: Bacterial Leucyl Aminopeptidase
Chain: A
Fragment: Residues 107-397
Ec: 3.4.11.10
Engineered: Yes
Mutation: Yes
Organism_scientific: Vibrio Proteolyticus
Organism_taxid: 671
Strain: Dsm 30189 Ifo 13287 Lmg 3772 Ncimb 1326
Atcc: 15338
Gene: Aap
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b
symmetry Space Group: P 61 2 2
R_factor 0.149 R_Free 0.171
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.317 109.317 91.003 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.22 Å
ligand NA, SCN, VAL, ZN enzyme Hydrolase E.C.3.4.11.10 BRENDA
Primary referenceZinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus., Ataie NJ, Hoang QQ, Zahniser MP, Tu Y, Milne A, Petsko GA, Ringe D, Biochemistry. 2008 Jul 22;47(29):7673-83. Epub 2008 Jun 25. PMID:18576673
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (3b3v.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 3B3V
  • CSU: Contacts of Structural Units for 3B3V
  • Likely Quarternary Molecular Structure file(s) for 3B3V
  • Structure Factors (663 Kb)
  • Retrieve 3B3V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B3V from S2C, [Save to disk]
  • Re-refined 3b3v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3B3V 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 3B3V
  • 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 3B3V, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b3v_A] [3b3v]
  • SWISS-PROT database: [Q01693]
  • Domain organization of [AMPX_VIBPR] by SWISSPFAM
  • Other resources with information on 3B3V
  • Community annotation for 3B3V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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