2Q2T Ligase Dna date May 29, 2007
title Structure Of Chlorella Virus Dna Ligase-Adenylate Bound To A Phosphorylated Nick
authors C.D.Lima, J.Nandakumar, P.A.Nair, P.Smith, S.Shuman
compound source
Molecule: 5'-D(Tptpcpcpgpaptpapgptpgpgpgpgpt Apapt)-3';
Chain: B
Engineered: Yes
 Synthetic: Yes
Other_details: Chemically Synthesized.

Molecule: 5'-D(Aptptpgpcpgpapcp(Omc)Pc)-3'
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: Chemically Synthesized.

Molecule: 5'-D(Pcpapcptpaptpcpgpgpapa)-3'
Chain: D
Engineered: Yes
Synthetic: Yes
Other_details: Chemically Synthesized.

Molecule: Chlorella Virus Dna Ligase
Chain: A
Engineered: Yes
Organism_scientific: Paramecium Bursaria Chlorella Virus 1
Organism_taxid: 10506
Strain: Chlorella Virus
Gene: A544r
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.301 81.290 96.418 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand AMP, OMC enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for nick recognition by a minimal pluripotent DNA ligase., Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S, Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:17618295
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (2q2t.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 2Q2T
  • CSU: Contacts of Structural Units for 2Q2T
  • Likely Quarternary Molecular Structure file(s) for 2Q2T
  • Structure Factors (185 Kb)
  • Retrieve 2Q2T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q2T from S2C, [Save to disk]
  • Re-refined 2q2t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2Q2T 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 2Q2T
  • 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 2Q2T, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q2t_C] [2q2t_D] [2q2t_B] [2q2t_A] [2q2t]
  • SWISS-PROT database: [O41026]
  • Domain organization of [O41026_PBCV1] by SWISSPFAM
    • Other resources with information on 2Q2T
  • Community annotation for 2Q2T 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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