1DUH Rna date Jan 17, 2000
title Crystal Structure Of The Conserved Domain Iv Of E. Coli 4.5s Rna
authors L.Jovine, T.Hainzl, C.Oubridge, W.G.Scott, J.Li, T.K.Sixma, A.Wonacott, T.Skarzynski, K.Nagai
compound source
Molecule: 4.5s Rna Domain Iv
Chain: A
Fragment: Domain Iv
Engineered: Yes
Synthetic: Yes
Other_details: Rna Sequence Taken From Escherichia Coli 4.5s Rna. The Rna Was Produced By T7 Rna Polymerase In Vitro Transcription Using Ribozyme Technology
symmetry Space Group: P 32 2 1
R_factor 0.230 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
69.697 69.697 84.102 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand LU, MG, PGP, SO4 enzyme
Primary referenceCrystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA., Jovine L, Hainzl T, Oubridge C, Scott WG, Li J, Sixma TK, Wonacott A, Skarzynski T, Nagai K, Structure Fold Des 2000 May 15;8(5):527-40. PMID:10801497
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (1duh.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 1DUH
  • CSU: Contacts of Structural Units for 1DUH
  • Likely Quarternary Molecular Structure file(s) for 1DUH
  • Structure Factors (127 Kb)
  • Retrieve 1DUH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DUH from S2C, [Save to disk]
  • Re-refined 1duh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DUH 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 1DUH
  • 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 1DUH, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Fold representative 1duh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1duh_A] [1duh]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 1DUH
  • Community annotation for 1DUH 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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