4R65 Transferase Dna date Aug 22, 2014
title Ternary Complex Crystal Structure Of R258a Mutant Of Dna Pol Beta
authors V.K.Batra, W.A.Beard, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl-11

Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
Fragment: Template Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Fragment: Primer Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Fragment: Downstream Primer Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.187 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.810 79.940 55.480 90.00 107.30 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CL, DUP, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSubstrate-Induced DNA Polymerase beta Activation., Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH, J Biol Chem. 2014 Sep 26. pii: jbc.M114.607432. PMID:25261471
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (4r65.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 4R65
  • CSU: Contacts of Structural Units for 4R65
  • Structure Factors (491 Kb)
  • Retrieve 4R65 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R65 from S2C, [Save to disk]
  • Re-refined 4r65 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R65 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 4R65
  • 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 4R65, from MSDmotif at EBI
  • Fold representative 4r65 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r65_T] [4r65_P] [4r65_D] [4r65_A] [4r65]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4R65: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4R65
  • Community annotation for 4R65 at PDBWiki (http://pdbwiki.org)

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