2IRY Transferase date Oct 16, 2006
title Crystal Structure Of The Polymerase Domain From Mycobacteriu Tuberculosis Ligase D With Dgtp And Manganese.
authors N.C.Brissett, R.S.Pitcher, A.J.Doherty
compound source
Molecule: Dna Ligase-Like Protein Rv0938mt0965
Chain: A, B
Fragment: Ligd Polymerase Domain (Residues 1-300)
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 83332
Strain: H37rv
Gene: Rv0938
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 1 21 1
R_factor 0.182 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.221 75.870 95.809 90.00 92.59 90.00
method X-Ray Diffractionresolution 1.78 Å
ligand DGT, MN enzyme Transferase E.C.2.7.7 BRENDA
Primary referenceStructure and Function of a Mycobacterial NHEJ DNA Repair Polymerase., Pitcher RS, Brissett NC, Picher AJ, Andrade P, Juarez R, Thompson D, Fox GC, Blanco L, Doherty AJ, J Mol Biol. 2006 Oct 20;. PMID:17174332
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (2iry.pdb1.gz) 52 Kb
  • Biological Unit Coordinates (2iry.pdb2.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 2IRY
  • CSU: Contacts of Structural Units for 2IRY
  • Likely Quarternary Molecular Structure file(s) for 2IRY
  • Structure Factors (414 Kb)
  • Retrieve 2IRY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IRY from S2C, [Save to disk]
  • Re-refined 2iry structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IRY 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 2IRY
  • 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 2IRY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2iry] [2iry_B] [2iry_A]
  • SWISS-PROT database: [P71571]
  • Domain organization of [Y938_MYCTU] by SWISSPFAM
  • Other resources with information on 2IRY
  • Community annotation for 2IRY 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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