3NAE Transferase Dna date Jun 01, 2010
title Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp Opposi Guanidinohydantoin
authors M.Wang, J.Beckman, G.Blaha, 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, Gp43
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: Dna (5'-D(Tpcpap(G35) Pgptpapapgpcpapgptpcpcpgpcpg)-3');
Chain: T
Engineered: Yes
Other_details: Template Dna Strand

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.013 119.783 130.727 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CA, DOC, DTP, G35 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 referenceSubstitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP and dGMP To Be Inserted opposite Guanidinohydantoin ., Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH, Biochemistry. 2010 Sep 9. PMID:20795733
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (3nae.pdb1.gz) 180 Kb
  • LPC: Ligand-Protein Contacts for 3NAE
  • CSU: Contacts of Structural Units for 3NAE
  • Structure Factors (1176 Kb)
  • Retrieve 3NAE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NAE from S2C, [Save to disk]
  • Re-refined 3nae structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NAE 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 3NAE
  • 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 3NAE, from MSDmotif at EBI
  • Fold representative 3nae from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nae_P] [3nae_T] [3nae] [3nae_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NAE: [POLBc ] by SMART
  • Other resources with information on 3NAE
  • Community annotation for 3NAE 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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