3BY5 Biosynthetic Protein date Jan 15, 2008
title Crystal Structure Of Cobalamin Biosynthesis Protein Chig Fro Agrobacterium Tumefaciens Str. C58
authors Y.Patskovsky, J.B.Bonanno, S.Sojitra, M.Rutter, M.Iizuka, M.Malet S.R.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx R Center For Structural Genomics (Nysgxrc)
compound source
Molecule: Cobalamin Biosynthesis Protein
Chain: A
Synonym: Protein Agr_c_5076p
Engineered: Yes
 Organism_scientific: Agrobacterium Tumefaciens Str.
Organism_taxid: 176299
Strain: C58
Atcc: 33970
Gene: Chig
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet
Expression_system_plasmid: Bc-Psgx3(Bc)
symmetry Space Group: H 3 2
R_factor 0.211 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.023 72.023 141.069 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.52 Å
ligand MSE, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (23 Kb) [Save to disk]
  • Biological Unit Coordinates (3by5.pdb1.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 3BY5
  • CSU: Contacts of Structural Units for 3BY5
  • Likely Quarternary Molecular Structure file(s) for 3BY5
  • Structure Factors (100 Kb)
  • Retrieve 3BY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BY5 from S2C, [Save to disk]
  • Re-refined 3by5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3BY5 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 3BY5
  • 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 3BY5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3by5] [3by5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3BY5
  • Community annotation for 3BY5 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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