4C8N Transferase Dna date Oct 01, 2013
title Binary Complex Of The Large Fragment Of Dna Polymerase I Fro Aquaticus With The Aritificial Base Pair Dnam-D5sics At The Postinsertion Site (Sequence Context 3)
authors K.Betz, D.A.Malyshev, T.Lavergne, W.Welte, K.Diederichs, F.E.Rome A.Marx
compound source
Molecule: Large Fragment Of Taq Dna Polymerase I
Chain: A
Fragment: Klenow Fragment, Residues 293-832
Synonym: Taq Polymerase 1, Large Fragment Of Taq Dna Polyme
Engineered: Yes
Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgdr11

Molecule: Primer, 5'-D(Apcpcpapcpgpgpcpgpcplhop)
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Template, 5'- D(Tptpgpbmnpgpcpgpcpcpgptpgpgptp)-3';
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 2 2 21
R_factor 0.196 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
65.617 101.096 204.316 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.88 Å
ligand BMN, LHO, PGE, SO4 enzyme Transferase E.C. BRENDA

Primary referenceStructural Insights into DNA Replication without Hydrogen Bonds., Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A, J Am Chem Soc. 2013 Nov 27. PMID:24283923
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (196 Kb) [Save to disk]
  • Biological Unit Coordinates (4c8n.pdb1.gz) 190 Kb
  • LPC: Ligand-Protein Contacts for 4C8N
  • CSU: Contacts of Structural Units for 4C8N
  • Structure Factors (492 Kb)
  • Retrieve 4C8N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4C8N from S2C, [Save to disk]
  • Re-refined 4c8n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4C8N 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 4C8N
  • 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 4C8N, from MSDmotif at EBI
  • Fold representative 4c8n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4c8n_C] [4c8n_A] [4c8n] [4c8n_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4C8N: [POLAc ] by SMART
  • Other resources with information on 4C8N
  • Community annotation for 4C8N at PDBWiki (http://pdbwiki.org)

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