2Q2U Ligase Dna date May 29, 2007
title Structure Of Chlorella Virus Dna Ligase-Product Dna Complex
authors C.D.Lima, J.Nandakumar, P.A.Nair, P.Smith, S.Shuman
compound source
Molecule: 5'-D(Tptpcpcpgpaptpapgptpgpgpgpgpt Apapt)-3';
Chain: E, G, I, K
Engineered: Yes
Synthetic: Yes
Other_details: Chemically Synthsized.

Molecule: 5'-D(Aptptpgpcpgpapcp(Omc) Pcpcpapcptpaptpcpgpgpapa)-3';
Chain: F, H, J, L
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthsized.

Molecule: Chlorella Virus Dna Ligase
Chain: A, B, C, D
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 1
R_factor 0.249 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.475 92.895 89.633 70.32 78.45 89.87
method X-Ray Diffractionresolution 3.00 Å
ligand OMC enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


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] (262 Kb) [Save to disk]
  • Biological Unit Coordinates (2q2u.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (2q2u.pdb2.gz) 67 Kb
  • Biological Unit Coordinates (2q2u.pdb3.gz) 66 Kb
  • Biological Unit Coordinates (2q2u.pdb4.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 2Q2U
  • CSU: Contacts of Structural Units for 2Q2U
  • Likely Quarternary Molecular Structure file(s) for 2Q2U
  • Structure Factors (329 Kb)
  • Retrieve 2Q2U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q2U from S2C, [Save to disk]
  • Re-refined 2q2u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q2U 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 2Q2U
  • 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 2Q2U, from MSDmotif at EBI
  • Fold representative 2q2u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q2u_E] [2q2u_I] [2q2u_J] [2q2u_A] [2q2u_D] [2q2u_K] [2q2u_B] [2q2u_L] [2q2u_F] [2q2u_G] [2q2u_C] [2q2u_H] [2q2u]
  • SWISS-PROT database: [O41026]
  • Domain organization of [O41026_PBCV1] by SWISSPFAM
  • Other resources with information on 2Q2U
  • Community annotation for 2Q2U 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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