3S9H Transferase Dna date Jun 01, 2011
title Rb69 Dna Polymerase Triple Mutant(L561as565gy567a) Ternary With Dupnpp And A Dideoxy-Terminated Primer In The Presence
authors M.Wang, J.Wang, W.H.Konigsberg
compound source
Molecule: 5'-D(Tpcpapapgptpapapgpcpapgptpcpc -3';
Chain: T
Engineered: Yes
Other_details: Template Dna Strand
Synthetic: Yes

Molecule: 5'-D(Gpcpgpgpapcptpgpcptptpap(Doc))-
Chain: P
Engineered: Yes
Other_details: Primer Dna Strand

Synthetic: Yes

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

Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43, Gp43
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 21b
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.050 119.821 130.791 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CA, DOC, DUP 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 referenceStructural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase., Xia S, Wang M, Blaha G, Konigsberg WH, Wang J, Biochemistry. 2011 Oct 25;50(42):9114-24. Epub 2011 Sep 29. PMID:21923197
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (360 Kb) [Save to disk]
  • Biological Unit Coordinates (3s9h.pdb1.gz) 352 Kb
  • LPC: Ligand-Protein Contacts for 3S9H
  • CSU: Contacts of Structural Units for 3S9H
  • Structure Factors (1266 Kb)
  • Retrieve 3S9H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3S9H from S2C, [Save to disk]
  • Re-refined 3s9h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3S9H 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 3S9H
  • 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 3S9H, from MSDmotif at EBI
  • Fold representative 3s9h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3s9h_T] [3s9h] [3s9h_A] [3s9h_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3S9H: [POLBc ] by SMART
  • Other resources with information on 3S9H
  • Community annotation for 3S9H at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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