4M0A Transferase Dna date Aug 01, 2013
title Human Dna Polymerase Mu Post-Catalytic 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: Unp Residues 132-494
Synonym: Pol Mu, Terminal Transferase
Ec: 2.7.7.7
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 0.163 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.018 68.670 110.444 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand EDO, EPE, MG, MN, PPV enzyme Transferase E.C.2.7.7.7 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] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (4m0a.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 4M0A
  • CSU: Contacts of Structural Units for 4M0A
  • Structure Factors (508 Kb)
  • Retrieve 4M0A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M0A from S2C, [Save to disk]
  • Re-refined 4m0a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4M0A 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 4M0A
  • 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 4M0A, from MSDmotif at EBI
  • Fold representative 4m0a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m0a_A] [4m0a_D] [4m0a] [4m0a_P] [4m0a_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4M0A: [POLXc ] by SMART
  • Other resources with information on 4M0A
  • Community annotation for 4M0A at PDBWiki (http://pdbwiki.org)

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