3K59 Transferase Dna date Oct 06, 2009
title Crystal Structure Of E.Coli Pol II-Normal Dna-Dctp Ternary C
authors W.Yang, F.Wang
compound source
Molecule: Dna Polymerase II
Chain: A
Synonym: Pol II
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12
Gene: B0060, Dina, Jw0059, Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet28 With Prescission Cleavage Site;

Molecule: Dna (5'- D(Tpapgpgptpapcpgpcptpapgpgpcpapcpa)-3');
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Synthesis

Molecule: Dna (5'-D(Gptpgpcpcptpapgpcpgptpap(D
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Synthesis
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.726 100.656 126.030 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.92 Å
ligand DCP, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • 3'-5'-exodeoxyribonuclease a...


  • Primary referenceStructural insight into translesion synthesis by DNA Pol II., Wang F, Yang W, Cell. 2009 Dec 24;139(7):1279-89. PMID:20064374
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (3k59.pdb1.gz) 151 Kb
  • LPC: Ligand-Protein Contacts for 3K59
  • CSU: Contacts of Structural Units for 3K59
  • Structure Factors (511 Kb)
  • Retrieve 3K59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K59 from S2C, [Save to disk]
  • Re-refined 3k59 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K59 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 3K59
  • 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 3K59, from MSDmotif at EBI
  • Fold representative 3k59 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k59_P] [3k59_A] [3k59] [3k59_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3K59: [POLBc ] by SMART
  • Other resources with information on 3K59
  • Community annotation for 3K59 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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