3PVV 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)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19pps

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

Synthetic: Yes

Molecule: Dna (5'-D(Gptptpgptpgpgpapcpapapcpg)
Chain: D, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 32 2 1
R_factor 0.251 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.441 88.441 105.156 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 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] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (3pvv.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (3pvv.pdb2.gz) 57 Kb
  • CSU: Contacts of Structural Units for 3PVV
  • Structure Factors (581 Kb)
  • Retrieve 3PVV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PVV from S2C, [Save to disk]
  • Re-refined 3pvv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PVV 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 3PVV
  • 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 3PVV, from MSDmotif at EBI
  • Fold representative 3pvv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pvv_C] [3pvv_A] [3pvv_E] [3pvv] [3pvv_F] [3pvv_D] [3pvv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PVV: [Bac_DnaA_C ] by SMART
  • Other resources with information on 3PVV
  • Community annotation for 3PVV 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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