4F4W Transferase Dna date May 11, 2012
title Y-Family Dna Polymerase Chimera Dbh-Dpo4-Dpo4 #1
authors J.D.Pata, R.C.Wilson
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Acidocaldarius, Sulfolobus Solfataricus;
Organism_taxid: 330779, 273057
Strain: Atcc 35092 Dsm 1617 Jcm 11322 P2
Gene: Dbh, Dpo4, Dpo4 (S. Solfataricus) And Dbh (S. Acidoca Saci_0554, Sso24 48;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr(De3)Plyss
Expression_system_vector_type: Pkkt7-H

Molecule: Dna (5'-D(Gpgpcpapcptpgpaptpcpgpgpc)
Chain: P, E
Engineered: Yes
Other_details: Primer Dna

Synthetic: Yes

Molecule: Dna (5'- D(Tptpapcpgpgpcpcpgpaptpcpapgptpgpcpc)-3'
Chain: T, F
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.187 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.820 99.655 101.625 90.00 90.16 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CA, DCP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene SACI
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceY-Family Polymerase Conformation Is a Major Determinant of Fidelity and Translesion Specificity., Wilson RC, Jackson MA, Pata JD, Structure. 2012 Dec 11. pii: S0969-2126(12)00420-0. doi:, 10.1016/j.str.2012.11.005. PMID:23245850
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (266 Kb) [Save to disk]
  • Biological Unit Coordinates (4f4w.pdb1.gz) 130 Kb
  • Biological Unit Coordinates (4f4w.pdb2.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 4F4W
  • CSU: Contacts of Structural Units for 4F4W
  • Structure Factors (610 Kb)
  • Retrieve 4F4W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F4W from S2C, [Save to disk]
  • Re-refined 4f4w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F4W 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 4F4W
  • 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 4F4W, from MSDmotif at EBI
  • Fold representative 4f4w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f4w_P] [4f4w_T] [4f4w_B] [4f4w_A] [4f4w] [4f4w_F] [4f4w_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4F4W
  • Community annotation for 4F4W at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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