3PVP Dna Binding Protein Dna date Dec 07, 2010
title Structure Of Mycobacterium Tuberculosis Dnaa-Dbd In Complex Dna
authors O.V.Tsodikov, T.Biswas
compound source
Molecule: Chromosomal Replication Initiator Protein Dnaa
Chain: A, B
Fragment: Dnaa Dbd
Engineered: Yes
 Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 419947
Strain: Atcc 25177 H37ra
Gene: Dnaa, Mra_0001, Rv0001
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)

Molecule: Dna (5'-D(Cpgptptpaptpcpcpapcpapapc)
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Gptptpgptpgpgpaptpapapcpg)
Chain: D, F
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 32 2 1
R_factor 0.221 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.677 88.677 105.162 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
Gene MRA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA., Tsodikov OV, Biswas T, J Mol Biol. 2011 May 18. PMID:21620858
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (3pvp.pdb1.gz) 55 Kb
  • Biological Unit Coordinates (3pvp.pdb2.gz) 56 Kb
  • CSU: Contacts of Structural Units for 3PVP
  • Structure Factors (171 Kb)
  • Retrieve 3PVP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PVP from S2C, [Save to disk]
  • Re-refined 3pvp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3PVP 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 3PVP
  • 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 3PVP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pvp_D] [3pvp_C] [3pvp_E] [3pvp_A] [3pvp_B] [3pvp] [3pvp_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PVP: [Bac_DnaA_C ] by SMART
    • Other resources with information on 3PVP
  • Community annotation for 3PVP 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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