2XCP Dna Transferase date Apr 24, 2010
title Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna Polymera Dihydro-8-Oxodeoxyguanine Modified Dna And Dctp - Magnesium
authors A.Irimia, M.Egli
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Gene: Dpo4
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22bdpo4-Nhis

Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptp Tpdoc)-3
Chain: E, P
Engineered: Yes
Other_details: 13-Mer Primer

Synthetic: Yes

Molecule: 5'-D(Tpcpapcp8ogpgpapaptpcpcp Tptpcpcpcpcpc)-3';
Chain: F, T
Engineered: Yes
Other_details: 18-Mer Template

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.757 100.429 105.873 90.00 96.08 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 8OG, DCP, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMetal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus., Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Sep 1;66(Pt, 9):1013-8. Epub 2010 Aug 21. PMID:20823515
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (2xcp.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (2xcp.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 2XCP
  • CSU: Contacts of Structural Units for 2XCP
  • Structure Factors (271 Kb)
  • Retrieve 2XCP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XCP from S2C, [Save to disk]
  • Re-refined 2xcp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XCP 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 2XCP
  • 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
  • 3D motif for 2XCP, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xcp_B] [2xcp_F] [2xcp_T] [2xcp] [2xcp_A] [2xcp_E] [2xcp_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2XCP
  • Community annotation for 2XCP 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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