5JH0 Dna Binding Protein date Apr 20, 2016
title Crystal Structure Of The Mitochondrial Dna Packaging Protein Complex With Dna At 2.18 Angstrom Resolution
authors A.Chakraborty, S.Lyonnais, M.Sola
compound source
Molecule: Ars-Binding Factor 2, Mitochondrial
Chain: A, D
Fragment: Unp Residues 27-183
Engineered: Yes
Other_details: Yeast Mitochondrial Dna Packaging Protein
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

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

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Dna (5'- D(Tptpaptpaptptpaptpaptpapaptptptpaptptp 3');
Chain: C, F
Engineered: Yes
Other_details: Dna

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
symmetry Space Group: C 1 2 1
R_factor 0.209 R_Free 0.236
length a length b length c angle alpha angle beta angle gamma
88.490 113.410 67.710 90.00 103.80 90.00
method X-Ray Diffractionresolution 2.18 Å
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] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (5jh0.pdb1.gz) 92 Kb
  • CSU: Contacts of Structural Units for 5JH0
  • Structure Factors (453 Kb)
  • Retrieve 5JH0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JH0 from S2C, [Save to disk]
  • Re-refined 5jh0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JH0 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 5JH0
  • 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
  • Fold representative 5jh0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jh0_B] [5jh0_E] [5jh0_A] [5jh0_C] [5jh0] [5jh0_D] [5jh0_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5JH0
  • Community annotation for 5JH0 at PDBWiki (http://pdbwiki.org)

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