2DKJ Transferase date Apr 11, 2006
title Crystal Structure Of T.Th.Hb8 Serine Hydroxymethyltransferas
authors K.Kai, M.Goto, I.Miyahara, K.Hirotsu, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Serine Hydroxymethyltransferase
Chain: A, B
Ec: 2.1.2.1
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 1 21 1
R_factor 0.180 R_Free 0.190
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.988 82.884 94.074 90.00 91.67 90.00
method X-Ray Diffractionresolution 1.15 Å
ligand PLP, SO4 enzyme Transferase E.C.2.1.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (2dkj.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 2DKJ
  • CSU: Contacts of Structural Units for 2DKJ
  • Likely Quarternary Molecular Structure file(s) for 2DKJ
  • Structure Factors (2412 Kb)
  • Retrieve 2DKJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DKJ from S2C, [Save to disk]
  • Re-refined 2dkj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2DKJ 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 2DKJ
  • 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 2DKJ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dkj] [2dkj_B] [2dkj_A]
  • SWISS-PROT database: [Q5SI56]
  • Domain organization of [GLYA_THET8] by SWISSPFAM
    • Other resources with information on 2DKJ
  • Community annotation for 2DKJ 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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