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
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 0.164 R_Free 0.196
crystal
cell
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.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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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