399D Dna date May 11, 1998
title Structure Of D(Cgcccgcgggcg)
authors L.Malinina, L.G.Fernandez, J.A.Subirana
compound source
Molecule: Dna (5'-D(Cpgpcpcpcpgpcpgpgpgpcpg)-3'
Chain: A, B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
31.290 42.602 45.995 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
Primary referenceStructure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features., Malinina L, Fernandez LG, Huynh-Dinh T, Subirana JA, J Mol Biol 1999 Jan 29;285(4):1679-90. PMID:9917405
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (14 Kb) [Save to disk]
  • Biological Unit Coordinates (399d.pdb1.gz) 11 Kb
  • CSU: Contacts of Structural Units for 399D
  • Likely Quarternary Molecular Structure file(s) for 399D
  • Structure Factors (34 Kb)
  • Retrieve 399D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 399D from S2C, [Save to disk]
  • Re-refined 399d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 399D 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 399D
  • 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 399D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [399d] [399d_A] [399d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 399D
  • Community annotation for 399D 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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