5BOX Dna Binding Protein date May 27, 2015
title Structure Of Trmbl2, An Archaeal Chromatin Protein, Shows A Of Dna Binding.
authors M.U.Ahmad, K.Diederichs, W.Welte
compound source
Molecule: Putative Hth-Type Transcriptional Regulator Trmbl
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Trmbl2, Pf0496
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet24d

Molecule: Dna Tgm (25-Mer)
Chain: E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261

Molecule: Dna (25-Mer)
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
symmetry Space Group: P 1 21 1
R_factor 0.224 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.619 105.790 93.235 90.00 96.75 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand GOL, MPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural insights into nonspecific binding of DNA by TrmBL2, an archaeal chromatin protein., Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W, J Mol Biol. 2015 Aug 20. pii: S0022-2836(15)00458-1. doi:, 10.1016/j.jmb.2015.08.012. PMID:26299937
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (422 Kb) [Save to disk]
  • Biological Unit Coordinates (5box.pdb1.gz) 412 Kb
  • LPC: Ligand-Protein Contacts for 5BOX
  • CSU: Contacts of Structural Units for 5BOX
  • Structure Factors (848 Kb)
  • Retrieve 5BOX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BOX from S2C, [Save to disk]
  • Re-refined 5box structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5BOX 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 5BOX
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5box_B] [5box_F] [5box_C] [5box_D] [5box_A] [5box_E] [5box]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5BOX
  • Community annotation for 5BOX at PDBWiki (http://pdbwiki.org)

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