6D33 Transferase date Apr 14, 2018
title Crystal Structure Of Bh1352 2-Deoxyribose-5-Phosphate From B Halodurans
authors P.J.Stogios, T.Skarina, T.Kim, V.Yim, A.Yakunin, A.Savchenko
compound source
Molecule: Deoxyribose-Phosphate Aldolase
Chain: A, B, C, D, E, F
Synonym: Dera,2-Deoxy-D-Ribose 5-Phosphate Aldolase, Phosphodeoxyriboaldolase,Deoxyriboaldolase;
Ec: 4.1.2.4
Engineered: Yes
Organism_scientific: Bacillus Halodurans (Strain Atcc Baa-1 18197 Ferm 7344 Jcm 9153 C-125);
Organism_taxid: 272558
Strain: Atcc Baa-125 Dsm 18197 Ferm 7344 Jcm 9153 C
Gene: Deoc, Dra, Bh1352
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P15tv Lic
symmetry Space Group: C 1 2 1
R_factor 0.205 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
240.908 55.523 177.706 90.00 128.02 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand GOL, TRS enzyme Lyase E.C.4.1.2.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (433 Kb) [Save to disk]
  • Biological Unit Coordinates (6d33.pdb1.gz) 144 Kb
  • Biological Unit Coordinates (6d33.pdb2.gz) 141 Kb
  • Biological Unit Coordinates (6d33.pdb3.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 6D33
  • CSU: Contacts of Structural Units for 6D33
  • Structure Factors (526 Kb)
  • Retrieve 6D33 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D33 from S2C, [Save to disk]
  • View 6D33 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 6D33
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d33_B] [6d33_E] [6d33_D] [6d33_C] [6d33_F] [6d33_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D33
  • Community annotation for 6D33 at PDBWiki (http://pdbwiki.org)

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