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
Ec: 2.7.7.7
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
crystal
cell
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.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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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