1UPG Transcription Repressor date Sep 30, 2003
title Crystal Structure Of The Quorum-Sensing Protein Tram From Agrobacterium Tumefaciens
authors A.Vannini, S.Di Marco
compound source
Molecule: Transcriptional Repressor Tram
Chain: A, B
Synonym: Tram
Engineered: Yes
 Organism_scientific: Agrobacterium Tumefaciens
Organism_taxid: 358
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_plasmid: Pt7.7
Other_details: Synthetic Gene
symmetry Space Group: P 21 21 2
R_factor 0.186 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.436 47.097 47.469 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.8 Å
ligand MSE enzyme
related structures by homologous chain: 1US6
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the quorum-sensing protein TraM and its interaction with the transcriptional regulator TraR., Vannini A, Volpari C, Di Marco S, J Biol Chem 2004 Jun 4;279(23):24291-6. Epub 2004 Mar 24. PMID:15044488
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (1upg.pdb1.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 1UPG
  • CSU: Contacts of Structural Units for 1UPG
  • Likely Quarternary Molecular Structure file(s) for 1UPG
  • Structure Factors (148 Kb)
  • Retrieve 1UPG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UPG from S2C, [Save to disk]
  • Re-refined 1upg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1UPG 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 1UPG
  • 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 1UPG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1upga_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1upgb_, region B [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1upg] [1upg_B] [1upg_A]
  • SWISS-PROT database: [Q57471]
  • Domain organization of [TRAM_RHIRD] by SWISSPFAM
    • Other resources with information on 1UPG
  • Community annotation for 1UPG 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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