2R8H Replication, Transferase Dna date Sep 10, 2007
title Selectivity Of Nucleoside Triphosphate Incorporation Opposit Propanodeoxyguanosine (Pdg) By The Sulfolobus Solfataricus Polymerase Dpo4 Polymerase
authors Y.Wang, S.Saleh, L.J.Marnette, M.Egli, M.P.Stone
compound source
Molecule: Dna (5'- D(Dgpdgpdgpdgpdgpdapdapdgpdgpdapdtpdtpdc)-3');
Chain: P
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Dtpdcpdapdcp(P) Pdgpdapdapdtpdcpdcpdtpdtpdcpdcpdcpdcpdc)-3');
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iv
Chain: A
Synonym: Dpo4, Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dbh, Dpo4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Purified Using Heat Denaturation, Ni2+-Nitri Chromatography, And Ion-Exchange Chromatography
symmetry Space Group: P 21 21 2
R_factor 0.215 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.400 103.000 52.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.48 Å
ligand CA, DGT, P enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInsertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV., Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP, Biochemistry. 2008 Jul 15;47(28):7322-34. Epub 2008 Jun 19. PMID:18563918
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (2r8h.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 2R8H
  • CSU: Contacts of Structural Units for 2R8H
  • Likely Quarternary Molecular Structure file(s) for 2R8H
  • Structure Factors (127 Kb)
  • Retrieve 2R8H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R8H from S2C, [Save to disk]
  • Re-refined 2r8h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2R8H 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 2R8H
  • 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 2R8H, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r8h_P] [2r8h] [2r8h_T] [2r8h_A]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2R8H
  • Community annotation for 2R8H 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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