3QNN Transferase Dna date Feb 08, 2011
title Rb69 Dna Polymerase (Y567a) Ternary Complex With Dgt Opposit
authors S.Xia, M.Wang, J.Wang, W.H.Konigsberg
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_common: Bacteriophage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psp72

Molecule: Dna Template
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Oligo Was Synthesized At The Kect Facilities University).;

Molecule: Dna Primer
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Oligo Was Synthesized At The Kect Facilities University).
symmetry Space Group: P 21 21 21
R_factor 0.181 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.811 120.042 130.409 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.92 Å
ligand CA, DGT, DOC, YCO 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 referenceUsing a Fluorescent Cytosine Analogue tC(o) To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase., Xia S, Beckman J, Wang J, Konigsberg WH, Biochemistry. 2012 May 22. PMID:22616982
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (350 Kb) [Save to disk]
  • Biological Unit Coordinates (3qnn.pdb1.gz) 342 Kb
  • LPC: Ligand-Protein Contacts for 3QNN
  • CSU: Contacts of Structural Units for 3QNN
  • Structure Factors (1172 Kb)
  • Retrieve 3QNN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QNN from S2C, [Save to disk]
  • Re-refined 3qnn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QNN 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 3QNN
  • 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 3QNN, from MSDmotif at EBI
  • Fold representative 3qnn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qnn] [3qnn_A] [3qnn_P] [3qnn_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3QNN: [POLBc ] by SMART
  • Other resources with information on 3QNN
  • Community annotation for 3QNN at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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