2D4R Structural Genomics, Unknown Function date Oct 23, 2005
title Crystal Structure Of Ttha0849 From Thermus Thermophilus Hb8
authors M.Nakabayashi, N.Shibata, S.Kuramitsu, Y.Higuchi, Riken Structur Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Hypothetical Protein Ttha0849
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.300 86.490 109.580 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand MSE, SO4 enzyme
Primary referenceStructure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 A resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily., Nakabayashi M, Shibata N, Komori H, Ueda Y, Iino H, Ebihara A, Kuramitsu S, Higuchi Y, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2005 Dec 1;61(Pt, 12):1027-31. Epub 2005 Nov 5. PMID:16511226
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (2d4r.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (2d4r.pdb2.gz) 28 Kb
  • Biological Unit Coordinates (2d4r.pdb3.gz) 28 Kb
  • Biological Unit Coordinates (2d4r.pdb4.gz) 28 Kb
  • Biological Unit Coordinates (2d4r.pdb5.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 2D4R
  • CSU: Contacts of Structural Units for 2D4R
  • Likely Quarternary Molecular Structure file(s) for 2D4R
  • Structure Factors (915 Kb)
  • Retrieve 2D4R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D4R from S2C, [Save to disk]
  • Re-refined 2d4r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2D4R 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 2D4R
  • 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 2D4R, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d4r_D] [2d4r] [2d4r_C] [2d4r_A] [2d4r_B]
  • SWISS-PROT database: [Q5SK03]
  • Domain organization of [Q5SK03_THET8] by SWISSPFAM
    • Other resources with information on 2D4R
  • Community annotation for 2D4R 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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