4J2B Transferase Dna date Feb 04, 2013
title Rb69 Dna Polymerase L415g Ternary Complex
authors S.Xia, J.Wang, W.H.Konigsberg
compound source
Molecule: Dna Polymerase
Chain: A
Fragment: Rb69 Dna Polymerase
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 (5'- D(Tpcpgptpaptpapapgpcpapgptpcpcpgpcpg)-3'
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpapt)
Chain: P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.169 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.590 120.465 130.865 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 referenceAlteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics., Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH, Nucleic Acids Res. 2013 Oct;41(19):9077-89. doi: 10.1093/nar/gkt674. Epub 2013, Aug 5. PMID:23921641
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (347 Kb) [Save to disk]
  • Biological Unit Coordinates (4j2b.pdb1.gz) 340 Kb
  • LPC: Ligand-Protein Contacts for 4J2B
  • CSU: Contacts of Structural Units for 4J2B
  • Structure Factors (1037 Kb)
  • Retrieve 4J2B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4J2B from S2C, [Save to disk]
  • Re-refined 4j2b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4J2B 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 4J2B
  • 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 4J2B, from MSDmotif at EBI
  • Fold representative 4j2b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4j2b_A] [4j2b] [4j2b_T] [4j2b_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4J2B: [POLBc ] by SMART
  • Other resources with information on 4J2B
  • Community annotation for 4J2B at PDBWiki (http://pdbwiki.org)

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