1L5Y Transcription Regulator date Mar 08, 2002
title Crystal Structure Of Mg2+ Bef3-Bound Receiver Domain Of Sinorhizobium Meliloti Dctd
authors S.Park, M.Meyer, A.D.Jones, H.P.Yennawar, N.H.Yennawar, B.T.Nixon
compound source
Molecule: C4-Dicarboxylate Transport Transcriptional Regula Protein Dctd;
Chain: A, B
Fragment: Receiver Domain, Residues 2-143
Synonym: Dctdnl
Engineered: Yes
Mutation: Yes
Organism_scientific: Sinorhizobium Meliloti
Organism_taxid: 382
Gene: Dctd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt143e121k
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.005 76.837 77.853 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand BEF, BF2, BF4, GOL, MG, SO4 enzyme
related structures by homologous chain: 1L5Z
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceTwo-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain., Park S, Meyer M, Jones AD, Yennawar HP, Yennawar NH, Nixon BT, FASEB J 2002 Dec;16(14):1964-6. Epub 2002 Oct 4. PMID:12368235
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1l5y.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1L5Y
  • CSU: Contacts of Structural Units for 1L5Y
  • Likely Quarternary Molecular Structure file(s) for 1L5Y
  • Structure Factors (140 Kb)
  • Retrieve 1L5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L5Y from S2C, [Save to disk]
  • Re-refined 1l5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1L5Y 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 1L5Y
  • 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 1L5Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l5ya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1l5yb_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1l5y_A] [1l5y_B] [1l5y]
  • SWISS-PROT database: [P13632]
  • Domain organization of [DCTD_RHIME] by SWISSPFAM
  • Domain found in 1L5Y: [REC ] by SMART
  • Other resources with information on 1L5Y
  • Community annotation for 1L5Y 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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