5JGH Dna Binding Protein date Apr 20, 2016
title Crystal Structure Of The Mitochondrial Dna Packaging Protein Complex With Dna At 2.6 Angstrom Resolution
authors A.Chakraborty, S.Lyonnais, M.Sola
compound source
Molecule: Ars-Binding Factor 2, Mitochondrial
Chain: A, D, G, J
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Abf2, Him1, Ymr072w, Ym9916.11
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcri7a (Pet-28a Derivative)

Molecule: Dna (5'- D(Tptptpaptptpaptptptptpaptpaptptpaptpap 3');
Chain: B, E, H, K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
Other_details: Oligos Purchased From Biomers

Molecule: Dna (5'- D(Tptpaptpaptpapaptpaptpapapapaptpapaptp 3');
Chain: C, F, I, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
Other_details: Oligos Purchased From Biomers
symmetry Space Group: P 1 21 1
R_factor 0.227 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
71.989 131.991 71.994 90.00 103.21 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand ACT enzyme
Primary referenceDNA structure directs positioning of the mitochondrial genome packaging protein Abf2p., Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Sola M, Nucleic Acids Res. 2017 Jan 25;45(2):951-967. doi: 10.1093/nar/gkw1147. Epub 2016, Nov 29. PMID:27899643
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (184 Kb) [Save to disk]
  • Biological Unit Coordinates (5jgh.pdb1.gz) 90 Kb
  • Biological Unit Coordinates (5jgh.pdb2.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 5JGH
  • CSU: Contacts of Structural Units for 5JGH
  • Structure Factors (2536 Kb)
  • Retrieve 5JGH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JGH from S2C, [Save to disk]
  • Re-refined 5jgh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JGH 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 5JGH
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5jgh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jgh_E] [5jgh] [5jgh_K] [5jgh_A] [5jgh_L] [5jgh_H] [5jgh_J] [5jgh_C] [5jgh_F] [5jgh_G] [5jgh_D] [5jgh_B] [5jgh_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5JGH
  • Community annotation for 5JGH at PDBWiki (http://pdbwiki.org)

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