4Q43 Transferase Dna date Apr 13, 2014
title Polymerase-Damaged Dna Complex
authors J.Kottur, A.Sharma, D.T.Nair
compound source
Molecule: Dna Polymerase Iv
Chain: A, F
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
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(Tpcptp(Rdg) Pgpgpgptpcpcptpapgpgpapcpcpc)-3');
Chain: B, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Synthesized Dna Oligonucleotide

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Synthesized Dna Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.830 56.790 112.020 90.00 91.96 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand 0KX, MG, RDG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A


Primary referenceUnique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic., Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B, Pradeepkumar PI, Nair DT, Structure. 2015 Jan 6;23(1):56-67. doi: 10.1016/j.str.2014.10.019. Epub 2014 Dec , 11. PMID:25497730
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (4q43.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (4q43.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 4Q43
  • CSU: Contacts of Structural Units for 4Q43
  • Structure Factors (1449 Kb)
  • Retrieve 4Q43 in mmCIF format [Save to disk]
  • Re-refined 4q43 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q43 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 4Q43
  • 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 4Q43, from MSDmotif at EBI
  • Fold representative 4q43 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q43_B] [4q43_G] [4q43_C] [4q43_H] [4q43_F] [4q43] [4q43_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4Q43
  • Community annotation for 4Q43 at PDBWiki (http://pdbwiki.org)

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