5IIM Transferase Dna date Mar 01, 2016
title Crystal Structure Of The Pre-Catalytic Ternary Extension Com Dna Polymerase Lambda With An 8-Oxo-Dg:Da Base-Pair
authors M.J.Burak, K.E.Guja, M.Garcia-Diaz
compound source
Molecule: Dna Polymerase Lambda
Chain: A
Synonym: Pol Lambda,Dna Polymerase Beta-2,Pol Beta2,Dna Pol Kappa;
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (5'-D(Pgpcpcpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpapgptpapa)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpgpgpcpap(8og)Ptpapcptpg)-3
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.274 63.700 140.725 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.94 Å
ligand 8OG, DUP, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG., Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M, EMBO J. 2016 Aug 1. pii: e201694332. PMID:27481934
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (5iim.pdb1.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 5IIM
  • CSU: Contacts of Structural Units for 5IIM
  • Structure Factors (728 Kb)
  • Retrieve 5IIM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IIM from S2C, [Save to disk]
  • Re-refined 5iim structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IIM 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 5IIM
  • 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
  • Fold representative 5iim from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5iim_T] [5iim_D] [5iim] [5iim_A] [5iim_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IIM: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5IIM
  • Community annotation for 5IIM at PDBWiki (http://pdbwiki.org)

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