2C2R Polymerase date Sep 29, 2005
title Efficient And High Fidelity Incorporation Of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase Dpo4
authors A.Irimia, L.V.Loukachevitch, M.Egli
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: P2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22bdpo4-Nhis
Other_details: Gene Dpo4

Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Tptpc)-3'
Chain: P
Other_details: 13-Mer Primer Extended By Polymerase To A 14-Mer;

Synthetic: Yes

Molecule: 5'-D(Tpcpapc 8ogpgpapaptpcpcp Tptpcpcpcpcpc)-3';
Chain: T
Other_details: 18-Mer Template

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.251 R_Free 0.310
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.200 100.150 52.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand 8OG, CA, DCT, DOC enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceEfficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4., Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP, J Biol Chem. 2006 Jan 27;281(4):2358-72. Epub 2005 Nov 22. PMID:16306039
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2c2r.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 2C2R
  • CSU: Contacts of Structural Units for 2C2R
  • Likely Quarternary Molecular Structure file(s) for 2C2R
  • Structure Factors (121 Kb)
  • Retrieve 2C2R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C2R from S2C, [Save to disk]
  • Re-refined 2c2r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2C2R 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 2C2R
  • 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 2C2R, from MSDmotif at EBI
  • Fold representative 2c2r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c2r_A] [2c2r_T] [2c2r] [2c2r_P]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2C2R
  • Community annotation for 2C2R 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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