2D24 Hydrolase date Sep 02, 2005
title Crystal Structure Of Es Complex Of Catalytic-Site Mutant Xyl Streptomyces Olivaceoviridis E-86
authors R.Suzuki, A.Kuno, Z.Fujimoto, S.Ito, S.I.Kawahara, S.Kaneko, T.Has K.Taira
compound source
Molecule: Endo-1,4-Beta-D-Xylanase
Chain: A, B
Synonym: Glycoside Hydrolase Family 10 Xylanase
Ec: 3.2.1.8
Engineered: Yes
Mutation: Yes
Organism_scientific: Streptomyces Olivaceoviridis
Organism_taxid: 1921
Strain: E-86
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe60
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.704 94.090 138.366 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand GOL, SO4, XYS enzyme Hydrolase E.C.3.2.1.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86., Suzuki R, Fujimoto Z, Ito S, Kawahara S, Kaneko S, Taira K, Hasegawa T, Kuno A, J Biochem. 2009 Jul;146(1):61-70. Epub 2009 Mar 11. PMID:19279191
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (2d24.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (2d24.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2D24
  • CSU: Contacts of Structural Units for 2D24
  • Likely Quarternary Molecular Structure file(s) for 2D24
  • Structure Factors (711 Kb)
  • Retrieve 2D24 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D24 from S2C, [Save to disk]
  • Re-refined 2d24 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D24 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 2D24
  • 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 2D24, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d24_B] [2d24_A] [2d24]
  • SWISS-PROT database: [Q7SI98]
  • Domain organization of [Q7SI98_STROI] by SWISSPFAM
  • Domains found in 2D24: [Glyco_10] [RICIN ] by SMART
  • Other resources with information on 2D24
  • Community annotation for 2D24 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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