3GIJ Transferase Dna date Mar 05, 2009
title Dpo4 Extension Ternary Complex With Oxog(Syn)-A(Anti) And Ox A(Syn) Pairs
authors O.Rechkoblit, L.Malinina, D.J.Patel
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus P2
Organism_taxid: 273057
Strain: P2 Dsm 1617 Jcm 11322
Atcc: 35092
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-Ril(Stratagene)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 5'-D(Gptptpgpgpaptpgpgptpapgp(2da))-
Chain: D, H
Engineered: Yes
Other_details: Primer Strand (Dideoxy-Terminated At 3'-End)

Synthetic: Yes
Other_details: Dna Primer Strand

Molecule: 5'-D(Cptpapapcp(8og) Pcptpapcpcpaptpcpcpapapc)-3';
Chain: E, J
Engineered: Yes
Other_details: Oxog-Modified Template Strand

Synthetic: Yes
Other_details: Dna Oxog-Modified Template Strand
symmetry Space Group: P 1 21 1
R_factor 0.209 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.264 107.409 97.867 90.00 100.54 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 2DA, 8OG, CA, DGT enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceImpact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases., Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ, Structure. 2009 May 13;17(5):725-36. PMID:19446528
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (3gij.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (3gij.pdb2.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 3GIJ
  • CSU: Contacts of Structural Units for 3GIJ
  • Likely Quarternary Molecular Structure file(s) for 3GIJ
  • Structure Factors (284 Kb)
  • Retrieve 3GIJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GIJ from S2C, [Save to disk]
  • Re-refined 3gij structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GIJ 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 3GIJ
  • 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 3GIJ, from MSDmotif at EBI
  • Fold representative 3gij from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gij] [3gij_A] [3gij_E] [3gij_H] [3gij_D] [3gij_B] [3gij_J]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 3GIJ
  • Community annotation for 3GIJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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