4IRD Transferase Dna date Jan 14, 2013
title Structure Of Polymerase-Dna Complex
authors D.T.Nair, A.Sharma
compound source
Molecule: Dna (5'- D(Tpcptptpgpgpgptpcpcptpapgpgpapcpcpc)-3'
Chain: G, B
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Gpgpgptpcpcptpapgpgpapcpcp
Chain: H
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Cptpapgpgpgptpcpcptpapgpgpapcpcpc)-3');
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iv
Chain: F, 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
Expression_system_vector_type: Pgex6p1
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.690 56.880 110.930 90.00 93.99 90.00
method X-Ray Diffractionresolution 2.48 Å
ligand DZ4, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A


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] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (4ird.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (4ird.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 4IRD
  • CSU: Contacts of Structural Units for 4IRD
  • Structure Factors (1576 Kb)
  • Retrieve 4IRD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IRD from S2C, [Save to disk]
  • Re-refined 4ird structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IRD 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 4IRD
  • 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 4IRD, from MSDmotif at EBI
  • Fold representative 4ird from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ird] [4ird_C] [4ird_G] [4ird_H] [4ird_F] [4ird_B] [4ird_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IRD
  • Community annotation for 4IRD at PDBWiki (http://pdbwiki.org)

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