4M9J Transferase Dna date Aug 14, 2013
title Dna Polymerase Beta E295k Soaked With Dumpnpp
authors B.E.Eckenroth, S.Doublie
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_strain: Rosetta 2 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Dna Template Strand
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Dna Template Strand, 16mer

Molecule: Dna Primer Strand
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Dna Primer Strand, 10mer

Molecule: Dna Downstream Strand
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Dna Downstream Strand, 5mer
symmetry Space Group: P 1 21 1
R_factor 0.186 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.580 79.129 54.979 90.00 105.95 90.00
method X-Ray Diffractionresolution 2.04 Å
ligand CL, DUP, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe E295K cancer variant of human polymerase beta favors the mismatch conformational pathway during nucleotide selection., Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S, J Biol Chem. 2013 Oct 18. PMID:24133209
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (4m9j.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 4M9J
  • CSU: Contacts of Structural Units for 4M9J
  • Structure Factors (1742 Kb)
  • Retrieve 4M9J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M9J from S2C, [Save to disk]
  • Re-refined 4m9j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4M9J 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 4M9J
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4M9J, from MSDmotif at EBI
  • Fold representative 4m9j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m9j_D] [4m9j] [4m9j_P] [4m9j_A] [4m9j_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4M9J: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4M9J
  • Community annotation for 4M9J at PDBWiki (http://pdbwiki.org)

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