4C8O 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 2)
authors K.Betz, D.A.Malyshev, T.Lavergne, W.Welte, K.Diederichs, F.E.Rome A.Marx
compound source
Molecule: Dna Polymerase I, Thermostable
Chain: A
Fragment: Klenow Fragment, Residues 293-832
Synonym: Taq Polymerase 1
Engineered: Yes
Other_details: Open Conformation Of Enzyme Trapped By Cryst Contacts;
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: 5'-D(Gpcpcpapcpgpgpcpgpcplhop)-3'
Chain: B
Synonym: Primer
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tptpcpbmnpgpcpgpcpcpgptpgpgpcp
Chain: C
Synonym: Template
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 2 2 21
R_factor 0.185 R_Free 0.212
length a length b length c angle alpha angle beta angle gamma
64.802 99.185 203.602 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand BMN, CL, LHO, MG, SO4, TRS 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] (306 Kb) [Save to disk]
  • Biological Unit Coordinates (4c8o.pdb1.gz) 299 Kb
  • LPC: Ligand-Protein Contacts for 4C8O
  • CSU: Contacts of Structural Units for 4C8O
  • Structure Factors (591 Kb)
  • Retrieve 4C8O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4C8O from S2C, [Save to disk]
  • Re-refined 4c8o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4C8O 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 4C8O
  • 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 4C8O, from MSDmotif at EBI
  • Fold representative 4c8o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4c8o_C] [4c8o_A] [4c8o_B] [4c8o]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4C8O: [POLAc ] by SMART
  • Other resources with information on 4C8O
  • Community annotation for 4C8O at PDBWiki (http://pdbwiki.org)

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