6WIE Transferase Dna date Apr 09, 2020
title Post-Catalytic Nicked Complex Of Human Polymerase Mu On A Complementary Dna Double-Strand Break Substrate
authors A.M.Kaminski, T.A.Kunkel, L.C.Pedersen, K.Bebenek
compound source
Molecule: Dna-Directed Dnarna Polymerase Mu
Chain: A
Fragment: Unp Residues 132-494
Synonym: Pol Mu,Terminal Transferase
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polm, Polmu
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgexm

Molecule: Dna (5'-D(Cpgpgpcpapt)-3')
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Apcpg)-3')
Chain: U
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpgptpapt)-3')
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgpcpcpg)-3')
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.170 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.073 62.247 118.318 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand 1PE, CL, GOL, MG, NA, PEG, PPV, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Primary referenceStructural snapshots of human DNA polymerase mu engaged on a DNA double-strand break., Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K, Nat Commun. 2020 Sep 22;11(1):4784. doi: 10.1038/s41467-020-18506-5. PMID:32963245
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (6wie.pdb1.gz) 131 Kb
  • LPC: Ligand-Protein Contacts for 6WIE
  • CSU: Contacts of Structural Units for 6WIE
  • Structure Factors (437 Kb)
  • Retrieve 6WIE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6WIE from S2C, [Save to disk]
    • View 6WIE 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 6WIE
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6wie_D] [6wie_U] [6wie_P] [6wie_A] [6wie_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6WIE
  • Community annotation for 6WIE at PDBWiki (http://pdbwiki.org)

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