4B9N Transferase Dna date Sep 05, 2012
title Structure Of The High Fidelity Dna Polymerase I Correctly By The Oxidative Formamidopyrimidine-Da Dna Lesion.
authors T.H.Gehrke, U.Lischke, S.Arnold, S.Schneider, T.Carell
compound source
Molecule: Dna Polymerase
Chain: A
Ec: 2.7.7.7
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_plasmid: Pdest007

Molecule: 5'-D(Gpcpcptpgpapcptpcptptptptp)-3'
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422

Molecule: 5'-D(Cpapap(Fax)Apgpapgptpcpapgpgpc
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.452 93.726 105.265 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand FAX, FRU, GLC, MG, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • 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] (224 Kb) [Save to disk]
  • Biological Unit Coordinates (4b9n.pdb1.gz) 216 Kb
  • LPC: Ligand-Protein Contacts for 4B9N
  • CSU: Contacts of Structural Units for 4B9N
  • Structure Factors (340 Kb)
  • Retrieve 4B9N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B9N from S2C, [Save to disk]
  • Re-refined 4b9n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B9N 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 4B9N
  • 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 4B9N, from MSDmotif at EBI
  • Fold representative 4b9n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b9n_B] [4b9n_A] [4b9n] [4b9n_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4B9N: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4B9N
  • Community annotation for 4B9N at PDBWiki (http://pdbwiki.org)

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