3DNB Dna date Mar 18, 1988
title Helix Geometry, Hydration, And G.A Mismatch In A B-Dna Decam
authors G.G.Prive, R.E.Dickerson
compound source
Molecule: Dna (5'-D(Cpcpapapgpaptptpgpg)-3')
Chain: A
Engineered: Yes
 Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
32.520 26.170 34.300 90.00 118.90 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand MG enzyme
Primary referenceStructure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G., Prive GG, Yanagi K, Dickerson RE, J Mol Biol 1991 Jan 5;217(1):177-99. PMID:1988677
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (10 Kb) [Save to disk]
  • Biological Unit Coordinates (3dnb.pdb1.gz) 8 Kb
  • LPC: Ligand-Protein Contacts for 3DNB
  • CSU: Contacts of Structural Units for 3DNB
  • Likely Quarternary Molecular Structure file(s) for 3DNB
  • Structure Factors (81 Kb)
  • Retrieve 3DNB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DNB from S2C, [Save to disk]
  • Re-refined 3dnb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DNB 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 3DNB
  • 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 3DNB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dnb_A] [3dnb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3DNB
  • Community annotation for 3DNB 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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