4B9V Transferase Dna date Sep 06, 2012
title Structure Of The High Fidelity Dna Polymerase I With Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair.
authors T.H.Gehrke, U.Lischke, S.Arnold, S.Schneider, T.Carell
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Dna Polymerase I
Engineered: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_vector: Pdest007
Other_details: German Collection Of Microorganisms Dsm No.

Molecule: 5'-D(Cpcptpgpapcptpcptpapap)-3'
Chain: B
Other_details: Oxidative Dna Lesion Fapyg At C4

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422

Molecule: 5'-D(Cpaptpfoxpapgpapgptpcpapgpgpcp
Chain: C
Other_details: Oxidative Dna Lesion Fapyg At C4

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
symmetry Space Group: P 21 21 21
R_factor 0.18682 R_Free 0.21529
length a length b length c angle alpha angle beta angle gamma
87.901 94.035 105.341 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand FOX, MG, SO4 enzyme Transferase E.C. BRENDA
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity

  • Primary referenceUnexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions., Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T, Nat Chem Biol. 2013 May 19. doi: 10.1038/nchembio.1254. PMID:23685671
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (221 Kb) [Save to disk]
  • Biological Unit Coordinates (4b9v.pdb1.gz) 212 Kb
  • LPC: Ligand-Protein Contacts for 4B9V
  • CSU: Contacts of Structural Units for 4B9V
  • Structure Factors (358 Kb)
  • Retrieve 4B9V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B9V from S2C, [Save to disk]
  • Re-refined 4b9v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Visual 3D analysis of 4B9V
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  • 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 4B9V, from MSDmotif at EBI
  • Fold representative 4b9v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b9v_B] [4b9v_C] [4b9v_A] [4b9v]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4B9V: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4B9V
  • Community annotation for 4B9V at PDBWiki (http://pdbwiki.org)

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