5C5J Transferase Dna date Jun 20, 2015
title Poymerase Nucleotide Complex
authors D.T.Nair, J.Kottur
compound source
Molecule: Dna Polymerase Iv
Chain: F, A
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: [Number Sign]1h766
Gene: Dinb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p1

Molecule: Dna (5'- D(Tpcptpapgpgpgptpcpcptpapgpgpapcpcpc)-3'
Chain: G, H, B, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.222 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.450 57.380 110.640 90.00 94.51 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 8GT, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A


Primary referenceReactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics., Kottur J, Nair DT, Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2397-400. doi: 10.1002/anie.201509340. , Epub 2016 Jan 12. PMID:26757158
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (5c5j.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (5c5j.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 5C5J
  • CSU: Contacts of Structural Units for 5C5J
  • Structure Factors (4359 Kb)
  • Retrieve 5C5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C5J from S2C, [Save to disk]
  • Re-refined 5c5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C5J 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 5C5J
  • 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
  • Fold representative 5c5j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c5j_G] [5c5j_C] [5c5j_B] [5c5j] [5c5j_A] [5c5j_H] [5c5j_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5C5J
  • Community annotation for 5C5J at PDBWiki (http://pdbwiki.org)

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