3NM9 Gene Regulation Dna date Jun 22, 2010
title Hmgd(M13a)-Dna Complex
authors M.E.A.Churchill, J.Klass, D.L.Zoetewey
compound source
Molecule: High Mobility Group Protein D
Chain: A, D, G, J, M, P
Synonym: Hmg-D
Engineered: Yes
Mutation: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Cg17950, Hmgd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet13a
Expression_system_plasmid: Pet-D74-M13a

Molecule: Dna 5'-D(Ggpcpgpaptpaptpcpgpc)-3'
Chain: B, C, E, F, H, I, K, L, N, O
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1
R_factor 0.245 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.750 71.700 89.020 92.49 91.12 107.10
method X-Ray Diffractionresolution 2.85 Å
Primary referenceStructural Analysis of HMGD-DNA Complexes Reveals Influence of Intercalation on Sequence Selectivity and DNA Bending., Churchill ME, Klass J, Zoetewey DL, J Mol Biol. 2010 Aug 25. PMID:20800069
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (3nm9.pdb1.gz) 112 Kb
  • CSU: Contacts of Structural Units for 3NM9
  • Structure Factors (356 Kb)
  • Retrieve 3NM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NM9 from S2C, [Save to disk]
  • Re-refined 3nm9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NM9 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 3NM9
  • 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 3NM9, from MSDmotif at EBI
  • Fold representative 3nm9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nm9_P] [3nm9_E] [3nm9] [3nm9_J] [3nm9_L] [3nm9_C] [3nm9_N] [3nm9_I] [3nm9_D] [3nm9_G] [3nm9_O] [3nm9_F] [3nm9_K] [3nm9_M] [3nm9_H] [3nm9_B] [3nm9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NM9: [HMG ] by SMART
  • Other resources with information on 3NM9
  • Community annotation for 3NM9 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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