4M42 Hydrolase Dna date Aug 06, 2013
title Rb69 Dna Polymerase Ternary Complex With Dgdt At Position N Primertemplate Duplex
authors S.Xia, 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_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Template
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Oligo Was Synthesized At Keck Facilities. (Y University);

Molecule: Dna Primer
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Oligo Was Synthesized At Keck Facilities. (Y University)
symmetry Space Group: P 21 21 21
R_factor 0.185 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.538 118.657 130.651 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.04 Å
ligand ATP, CA 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 referenceMispairs with Watson-Crick Base-pair Geometry Observed in Ternary Complexes of an RB69 DNA Polymerase Variant., Xia S, Konigsberg WH, Protein Sci. 2014 Jan 24. doi: 10.1002/pro.2434. PMID:24458997
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (347 Kb) [Save to disk]
  • Biological Unit Coordinates (4m42.pdb1.gz) 340 Kb
  • LPC: Ligand-Protein Contacts for 4M42
  • CSU: Contacts of Structural Units for 4M42
  • Structure Factors (1451 Kb)
  • Retrieve 4M42 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M42 from S2C, [Save to disk]
  • Re-refined 4m42 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4M42 in 3D
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4M42
  • 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 4M42, from MSDmotif at EBI
  • Fold representative 4m42 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m42_P] [4m42] [4m42_A] [4m42_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4M42: [POLBc ] by SMART
  • Other resources with information on 4M42
  • Community annotation for 4M42 at PDBWiki (http://pdbwiki.org)

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