3CQ8 Transferase Dna date Apr 02, 2008
title Ternary Complex Of The L415f Mutant Rb69 Exo(-)Polymerase
authors X.Zhong, L.C.Pedersen, T.A.Kunkel
compound source
Molecule: Dna (5'- D(Dapdcpdapdgpdgpdtpdapdapdgpdcpdapdgpdtpdcp Pdg)-3');
Chain: T
Engineered: Yes
Other_details: Template Strand
Synthetic: Yes

Molecule: Dna (5'- D(Dgpdcpdgpdgpdapdcpdtpdgpdcpdtpdtpdapdcpdc)-
Chain: P
Engineered: Yes
Other_details: Dideoxy Terminated Primer Strand

Synthetic: Yes

Molecule: Dna Polymerase
Chain: A
Fragment: Rb69 Polymerase
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Enterobacteria Phage
Organism_taxid: 12353
Strain: Rb69
Gene: 43
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcw50
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.840 117.006 127.823 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CA, GOL, NA, TTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • Primary referenceCharacterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity., Zhong X, Pedersen LC, Kunkel TA, Nucleic Acids Res. 2008 Jul;36(12):3892-904. Epub 2008 May 24. PMID:18503083
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (178 Kb) [Save to disk]
  • Biological Unit Coordinates (3cq8.pdb1.gz) 168 Kb
  • LPC: Ligand-Protein Contacts for 3CQ8
  • CSU: Contacts of Structural Units for 3CQ8
  • Likely Quarternary Molecular Structure file(s) for 3CQ8
  • Structure Factors (607 Kb)
  • Retrieve 3CQ8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CQ8 from S2C, [Save to disk]
  • Re-refined 3cq8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CQ8 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 3CQ8
  • 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 3CQ8, from MSDmotif at EBI
  • Fold representative 3cq8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cq8_T] [3cq8_P] [3cq8] [3cq8_A]
  • SWISS-PROT database: [Q38087]
  • Domain organization of [DPOL_BPR69] by SWISSPFAM
  • Domain found in 3CQ8: [POLBc ] by SMART
  • Other resources with information on 3CQ8
  • Community annotation for 3CQ8 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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