2W8K Transferase Dna date Jan 16, 2009
title Y-Family Dna Polymerase Dpo4 Bypassing N2-Naphthyl-Guanine Adduct In Syn Orientation
authors R.L.Eoff, H.Zhang, M.Egli, F.P.Guengerich
compound source
Molecule: Dna Polymerase Iv
Chain: A
Ec: 2.7.7.7
Engineered: Yes
Other_details: Y-Family Dna Polymerase From Sulfolobus Solfataricus;
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Atcc: 35092
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet22b

Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Tptpcpdoc)-3';
Chain: P
Other_details: 14 Base Primer Dna 5'-Ggg Gga Agg Att Cc-3'

Synthetic: Yes

Molecule: 5'-D(Tpcpapcpn2gpgpapaptpcpcp Tptpcpcpcpcpc)-3';
Chain: T
Other_details: 18 Base Template Dna 5'-Tca C(N2g)G Aat Cct Tcc Ccc-3'

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.233 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.040 103.910 52.320 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand DGT, DOC, MG, N2G enzyme Transferase E.C.2.7.7.7 BRENDA
note 2W8K supersedes 2V4S
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceVersatility of Y-family sulfolobus solfataricus DNA polymerase Dpo4 in translesion synthesis past bulky N2-Alkyl guanine adducts., Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP, J Biol Chem. 2008 Dec 4. PMID:19059910
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (2w8k.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 2W8K
  • CSU: Contacts of Structural Units for 2W8K
  • Likely Quarternary Molecular Structure file(s) for 2W8K
  • Structure Factors (53 Kb)
  • Retrieve 2W8K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W8K from S2C, [Save to disk]
  • Re-refined 2w8k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W8K 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 2W8K
  • 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 2W8K, from MSDmotif at EBI
  • Fold representative 2w8k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w8k_T] [2w8k_P] [2w8k] [2w8k_A]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2W8K
  • Community annotation for 2W8K 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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