5TRD Transferase Dna date Oct 26, 2016
title Structure Of Rbkr (Riboflavin Kinase) From Thermoplasma Acid Determined In Complex With Ctp And Its Cognate Dna Operator
authors M.W.Vetting, I.A.Rodionova, X.Li, A.L.Osterman, D.A.Rodionov, S.C
compound source
Molecule: Riboflavin Kinase
Chain: A, B
Fragment: Riboflavin Kinase And Regulator
Synonym: Rfk,Ctp-Dependent Riboflavin Kinase,Ctp:Riboflavin Phosphotransferase,Flavokinase;
Ec: 2.7.1.161
Engineered: Yes
 Organism_scientific: Thermoplasma Acidophilum
Organism_taxid: 273075
Strain: Atcc 25905 Dsm 1728 Jcm 9062 Nbrc 15155 Amr
Gene: Ribk, Ta1064
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23 Derivative

Molecule: Dna (5'- D(Aptptpapcptpapaptptpcpapcpgpapgptpapa)
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermoplasma Acidophilum
Organism_taxid: 2303

Molecule: Dna (5'- D(Ptptptpapcptpcpgptpgpapaptptpapgptpapa
Chain: H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermoplasma Acidophilum
Organism_taxid: 2303
symmetry Space Group: P 1 21 1
R_factor 0.174 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.411 95.040 61.262 90.00 113.51 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand CTP, NA enzyme Transferase E.C.2.7.1.161 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (189 Kb) [Save to disk]
  • Biological Unit Coordinates (5trd.pdb1.gz) 181 Kb
  • LPC: Ligand-Protein Contacts for 5TRD
  • CSU: Contacts of Structural Units for 5TRD
  • Structure Factors (3202 Kb)
  • Retrieve 5TRD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TRD from S2C, [Save to disk]
  • Re-refined 5trd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5TRD 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 5TRD
  • 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: [5trd_G] [5trd_H] [5trd_A] [5trd_B] [5trd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5TRD
  • Community annotation for 5TRD at PDBWiki (http://pdbwiki.org)

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