1J1V Replication Dna date Dec 18, 2002
title Crystal Structure Of Dnaa Domainiv Complexed With Dnaabox Dna
authors N.Fujikawa, H.Kurumizaka, O.Nureki, T.Terada, M.Shirouzu, T.Katayama, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: 5'-D(Tpgptptpaptpcpcpapcpapgpg)-3'
Chain: B
Synonym: Dnaabox Dna
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Cpcptpgptpgpgpaptpapapcpa)-3'
Chain: C
Synonym: Dnaabox Dna
Engineered: Yes

Synthetic: Yes

Molecule: Chromosomal Replication Initiator Protein Dnaa
Chain: A
Fragment: Dna Binding Domain, Dnaa Domainiv
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Dnaa
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
Other_details: Cell-Free Protein Synthesis System
symmetry Space Group: P 41 21 2
R_factor 0.229 R_Free 0.249
length a length b length c angle alpha angle beta angle gamma
50.385 50.385 158.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand MSE enzyme

Primary referenceStructural basis of replication origin recognition by the DnaA protein., Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S, Nucleic Acids Res 2003 Apr 15;31(8):2077-86. PMID:12682358
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (1j1v.pdb1.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 1J1V
  • CSU: Contacts of Structural Units for 1J1V
  • Likely Quarternary Molecular Structure file(s) for 1J1V
  • Structure Factors (146 Kb)
  • Retrieve 1J1V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1J1V from S2C, [Save to disk]
  • Re-refined 1j1v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1J1V 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 1J1V
  • 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 1J1V, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1j1va_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1j1v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1j1v_C] [1j1v_A] [1j1v] [1j1v_B]
  • SWISS-PROT database: [P03004]
  • Domain organization of [DNAA_ECOLI] by SWISSPFAM
  • Domain found in 1J1V: [Bac_DnaA_C ] by SMART
  • Other resources with information on 1J1V
  • Community annotation for 1J1V 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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