4IRK Transferase Dna date Jan 14, 2013
title Structure Of Polymerase-Dna Complex, Dna
authors D.T.Nair, A.Sharma
compound source
Molecule: Dna Polymerase Iv
Chain: B, A
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: B0231, Dinb, Dinp, Jw0221
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41de3

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

Synthetic: Yes

Molecule: Dna (5'- D(Cptpagpgpgptpcpcptpapgpgpapcpcp(Doc))-3'
Chain: G, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.209 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.650 57.080 110.230 90.00 94.92 90.00
method X-Ray Diffractionresolution 2.32 Å
ligand DCP, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli., Sharma A, Kottur J, Narayanan N, Nair DT, Nucleic Acids Res. 2013 Mar 21. PMID:23525461
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (288 Kb) [Save to disk]
  • Biological Unit Coordinates (4irk.pdb1.gz) 141 Kb
  • Biological Unit Coordinates (4irk.pdb2.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 4IRK
  • CSU: Contacts of Structural Units for 4IRK
  • Structure Factors (1889 Kb)
  • Retrieve 4IRK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IRK from S2C, [Save to disk]
  • Re-refined 4irk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IRK 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 4IRK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4IRK, from MSDmotif at EBI
  • Fold representative 4irk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4irk_A] [4irk_H] [4irk] [4irk_C] [4irk_B] [4irk_F] [4irk_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IRK
  • Community annotation for 4IRK at PDBWiki (http://pdbwiki.org)

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