4M04 Transferase Dna date Aug 01, 2013
title Human Dna Polymerase Mu Ternary Complex
authors A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pede
compound source
Molecule: Dna-Directed Dnarna Polymerase Mu
Chain: A
Fragment: Polymerase Mu Loop2 Deletion Variant, Unp Residue
Synonym: Pol Mu, Terminal Transferase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polm, Polmu
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgexm

Molecule: Template Strand
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By Oligos Etc

Molecule: Upstream Primer Strand
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By Oligos Etc

Molecule: Downstream Primer Strand
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By Oligos Etc
symmetry Space Group: P 21 21 21
R_factor 0.164 R_Free 0.196
length a length b length c angle alpha angle beta angle gamma
59.892 68.467 109.773 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CL, DUP, EDO, EPE, MG, NA enzyme Transferase E.C. BRENDA

Primary referenceSustained active site rigidity during synthesis by human DNA polymerase mu., Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC, Nat Struct Mol Biol. 2014 Mar;21(3):253-60. doi: 10.1038/nsmb.2766. Epub 2014 Feb, 2. PMID:24487959
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (4m04.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4M04
  • CSU: Contacts of Structural Units for 4M04
  • Structure Factors (679 Kb)
  • Retrieve 4M04 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M04 from S2C, [Save to disk]
  • Re-refined 4m04 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4M04 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 4M04
  • 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 4M04, from MSDmotif at EBI
  • Fold representative 4m04 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m04] [4m04_T] [4m04_P] [4m04_A] [4m04_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4M04: [POLXc ] by SMART
  • Other resources with information on 4M04
  • Community annotation for 4M04 at PDBWiki (http://pdbwiki.org)

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