4JV1 Transferase Dna date Mar 25, 2013
title Ternary Complex Of Gamma-Ohpdg Adduct Modified Dna With Dna Primer) Polymerase Iv And Incoming Dgtp
authors S.Banerjee, G.Shanmugam, M.P.Stone
compound source
Molecule: Dna Polymerase Iv
Chain: A
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

Molecule: Dna (5'-D(Pcp(Hn1) Pgpapaptpcpcptptpcpcpcpcpc)-3');
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Gpgpgpgpgpapapgpgpaptptpc)
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.213 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.274 102.183 52.727 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA, DGT, HN1 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRing-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4., Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP, Chem Res Toxicol. 2013 Aug 16. PMID:23947567
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (4jv1.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 4JV1
  • CSU: Contacts of Structural Units for 4JV1
  • Structure Factors (296 Kb)
  • Retrieve 4JV1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JV1 from S2C, [Save to disk]
  • Re-refined 4jv1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JV1 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 4JV1
  • 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 4JV1, from MSDmotif at EBI
  • Fold representative 4jv1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jv1] [4jv1_B] [4jv1_C] [4jv1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4JV1
  • Community annotation for 4JV1 at PDBWiki (http://pdbwiki.org)

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