1VAV Lyase date Feb 19, 2004
title Crystal Structure Of Alginate Lyase Pa1167 From Pseudomonas At 2.0 A Resolution
authors M.Yamasaki, S.Moriwaki, O.Miyake, W.Hashimoto, K.Murata, B.Mikami
compound source
Molecule: Alginate Lyase Pa1167
Chain: A, B
Engineered: Yes
Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 208964
Strain: Pao1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a-Pa1167
symmetry Space Group: P 1 21 1
R_factor 0.187 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.359 70.219 67.299 90.00 94.77 90.00
method X-Ray Diffractionresolution 2.00 Å
Primary referenceStructure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold., Yamasaki M, Moriwaki S, Miyake O, Hashimoto W, Murata K, Mikami B, J Biol Chem. 2004 Jul 23;279(30):31863-72. Epub 2004 May 10. PMID:15136569
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (1vav.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (1vav.pdb2.gz) 39 Kb
  • CSU: Contacts of Structural Units for 1VAV
  • Likely Quarternary Molecular Structure file(s) for 1VAV
  • Structure Factors (305 Kb)
  • Retrieve 1VAV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VAV from S2C, [Save to disk]
  • Re-refined 1vav structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VAV 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 1VAV
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VAV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vava_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vavb_, region B [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vav_B] [1vav] [1vav_A]
  • SWISS-PROT database: [Q9I4H0]
  • Domain organization of [Q9I4H0_PSEAE] by SWISSPFAM
  • Other resources with information on 1VAV
  • Community annotation for 1VAV 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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