3A0N Lyase date Mar 23, 2009
title Crystal Structure Of D-Glucuronic Acid-Bound Alginate Lyase Chlorella Virus
authors K.Ogura, M.Yamasaki, T.Hashidume, T.Yamada, B.Mikami, W.Hashimoto
compound source
Molecule: Val-1
Chain: A
Fragment: C-Terminal Domain, Residues 106-349
Synonym: Alginate Lyase Val-1
Ec: 4.2.2.3
Engineered: Yes
Organism_scientific: Chlorella Virus
Organism_taxid: 31555
Strain: Cvk-2
Gene: Val-1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b
symmetry Space Group: P 21 21 21
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.488 71.046 99.316 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand BDP enzyme Lyase E.C.4.2.2.3 BRENDA
Primary referenceCrystal structure of family 14 polysaccharide lyase with pH-dependent modes of action., Ogura K, Yamasaki M, Yamada T, Mikami B, Hashimoto W, Murata K, J Biol Chem. 2009 Dec 18;284(51):35572-9. Epub . PMID:19846561
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (3a0n.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 3A0N
  • CSU: Contacts of Structural Units for 3A0N
  • Structure Factors (1336 Kb)
  • Retrieve 3A0N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A0N from S2C, [Save to disk]
  • Re-refined 3a0n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A0N 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 3A0N
  • 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 3A0N, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a0n_A] [3a0n]
  • SWISS-PROT database: [Q9DTZ2]
  • Domain organization of [Q9DTZ2_9PHYC] by SWISSPFAM
  • Other resources with information on 3A0N
  • Community annotation for 3A0N 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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