3L8B Transferase Dna date Dec 30, 2009
title Crystal Structure Of A Replicative Dna Polymerase Bound To The Oxidized Guanine Lesion Guanidinohydantoin
authors P.Aller, Y.Ye, S.S.Wallace, C.J.Burrows, S.Doublie
compound source
Molecule: Dna Polymerase
Chain: A, B
Synonym: Gp43
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_common: Bacteriophage Rb69
Organism_taxid: 12353
Gene: 43, Gp43
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Dna (5'-D(Apctp(G35) Ptptpapapgpcpapgptpcpcpgpcpg)-3');
Chain: C, E
Engineered: Yes
Other_details: Dna Template

Synthetic: Yes

Molecule: Dna (5'- D(Gpcpgpgpapcptpgpcptptpapa)-3');
Chain: D, F
Engineered: Yes
Other_details: Dna Primer

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.219 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
78.276 120.246 136.963 90.00 95.96 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand G35, SO4 enzyme Transferase E.C. BRENDA
A, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity

  • Primary referenceCrystal Structure of a Replicative DNA Polymerase Bound to the Oxidized Guanine Lesion Guanidinohydantoin (,)., Aller P, Ye Y, Wallace SS, J Burrows C, Doublie S, Biochemistry. 2010 Feb 25. PMID:20166752
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (341 Kb) [Save to disk]
  • Biological Unit Coordinates (3l8b.pdb1.gz) 171 Kb
  • Biological Unit Coordinates (3l8b.pdb2.gz) 169 Kb
  • LPC: Ligand-Protein Contacts for 3L8B
  • CSU: Contacts of Structural Units for 3L8B
  • Structure Factors (4116 Kb)
  • Retrieve 3L8B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L8B from S2C, [Save to disk]
  • Re-refined 3l8b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L8B 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 3L8B
  • 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 3L8B, from MSDmotif at EBI
  • Fold representative 3l8b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l8b_B] [3l8b] [3l8b_D] [3l8b_E] [3l8b_C] [3l8b_F] [3l8b_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3L8B: [POLBc ] by SMART
  • Other resources with information on 3L8B
  • Community annotation for 3L8B 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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