3LOC Transcription date Feb 03, 2010
title Crystal Structure Of Putative Transcriptional Regulator Ycdc
authors Y.V.Patskovsky, A.A.Knapik, V.Mennella, S.K.Burley, W.Minor, S.C. York Sgx Research Center For Structural Genomics (Nysgxrc)
compound source
Molecule: Hth-Type Transcriptional Regulator Rutr
Chain: A, B, C, D
Synonym: Rut Operon Repressor
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: B1013, Jw0998, Rutr, Ycdc
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: T7 Topo-Ct
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.020 139.610 156.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand MSE, URA enzyme
note 3LOC supersedes 1PB6
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (3loc.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (3loc.pdb2.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 3LOC
  • CSU: Contacts of Structural Units for 3LOC
  • Structure Factors (310 Kb)
  • Retrieve 3LOC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LOC from S2C, [Save to disk]
  • Re-refined 3loc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LOC 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 3LOC
  • 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 3LOC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3loc_A] [3loc_C] [3loc_D] [3loc_B] [3loc]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3LOC
  • Community annotation for 3LOC 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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