2D1P Translation date Aug 30, 2005
title Crystal Structure Of Heterohexameric Tusbcd Proteins, Which Are Crucial For The Trna Modification
authors T.Numata, S.Fukai, Y.Ikeuchi, T.Suzuki, O.Nureki
compound source
Molecule: Hypothetical Upf0163 Protein Yhen
Chain: A, D, G
Synonym: Tusd
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Yhen
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe80l

Molecule: Hypothetical Upf0116 Protein Yhem
Chain: B, E, H
Synonym: Tusc
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Yhem
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe80l

Molecule: Hypothetical Protein Yhel
Chain: C, F, I
Synonym: Tusb
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Yhel
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe80l
symmetry Space Group: P 41 21 2
R_factor 0.209 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
141.392 141.392 135.686 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand SO4 enzyme
note 2D1P is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, D, G


E, B, H


F, C, I


Primary referenceStructural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex., Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O, Structure. 2006 Feb;14(2):357-66. PMID:16472754
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (2d1p.pdb1.gz) 112 Kb
  • Biological Unit Coordinates (2d1p.pdb2.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 2D1P
  • CSU: Contacts of Structural Units for 2D1P
  • Likely Quarternary Molecular Structure file(s) for 2D1P
  • Structure Factors (2344 Kb)
  • Retrieve 2D1P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D1P from S2C, [Save to disk]
  • Re-refined 2d1p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D1P 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 2D1P
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2D1P, from MSDmotif at EBI
  • Fold representative 2d1p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d1p_A] [2d1p_G] [2d1p_B] [2d1p] [2d1p_I] [2d1p_H] [2d1p_D] [2d1p_C] [2d1p_E] [2d1p_F]
  • SWISS-PROT database: [P45530] [P45531] [P45532]
  • Domain organization of [TUSB_ECOLI] [TUSC_ECOLI] [TUSD_ECOLI] by SWISSPFAM
  • Other resources with information on 2D1P
  • Community annotation for 2D1P 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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