4RZR Transferase Dna date Dec 23, 2014
title Bypass Of A Bulky Adduct Dg1,8 By Dpo4
authors R.Vyas, Z.Suo
compound source
Molecule: Dna Polymerase Iv
Chain: A, D
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: Atcc 35092 Dsm 1617 Jcm 11322 P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: Dna (5'-D(Tptpgpc(2jv) Pgpapcptpgpgptpaptptpgpgpg)-3');
Chain: B, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: 18-Mer Dna Template

Molecule: Dna (5'-D(Pcpcpcpapaptpapcpcpapgptpc
Chain: C, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: 13-Mer Dna Template
symmetry Space Group: P 31
R_factor 0.199 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.397 56.397 288.776 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand 2JV, CA, DCP, GOL, NA, TRS enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceMechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase., Vyas R, Efthimiopoulos G, Tokarsky EJ, Malik CK, Basu AK, Suo Z, J Am Chem Soc. 2015 Sep 23;137(37):12131-42. doi: 10.1021/jacs.5b08027. Epub 2015, Sep 11. PMID:26327169
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (293 Kb) [Save to disk]
  • Biological Unit Coordinates (4rzr.pdb1.gz) 144 Kb
  • Biological Unit Coordinates (4rzr.pdb2.gz) 145 Kb
  • LPC: Ligand-Protein Contacts for 4RZR
  • CSU: Contacts of Structural Units for 4RZR
  • Structure Factors (989 Kb)
  • Retrieve 4RZR in mmCIF format [Save to disk]
  • Re-refined 4rzr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RZR 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 4RZR
  • 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 4rzr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rzr_D] [4rzr_E] [4rzr] [4rzr_A] [4rzr_C] [4rzr_F] [4rzr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4RZR
  • Community annotation for 4RZR at PDBWiki (http://pdbwiki.org)

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