2V4R Transferase date Sep 26, 2008
title Non-Productive Complex Of The Y-Family Dna Polymerase Dpo4 W Skipping The M1dg Adduct To Pair With The Next Template Cyt
authors R.L.Eoff, J.B.Stafford, J.Szekely, C.J.Rizzo, M.Egli, F.P.Guenger L.J.Marnett
compound source
Molecule: Dna Polymerase Iv
Chain: A
Engineered: Yes
Other_details: Y-Family Dna Polymerase From Sulfolobus Solf
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_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptptpc)-3'
Chain: P
Engineered: Yes
Other_details: 13 Base Primer Dna 5'-Ggg Gga Agg Att C-3'

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpcpapcpm1gpgpapaptpcpcp Tptpcpcpcpcpc)-3';
Chain: T
Engineered: Yes
Other_details: 18 Base Template Dna 5'-Tca C(M1g)G Aat Cct

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 2
R_factor 0.218 R_Free 0.273
length a length b length c angle alpha angle beta angle gamma
93.545 102.537 52.176 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CA, DGT, M1G enzyme Transferase E.C. BRENDA

Primary referenceStructural and Functional Analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed Bypass of the Malondialdehyde-deoxyguanosine Adduct., Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ, Biochemistry. 2009 Jun 4. PMID:19492857
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2v4r.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 2V4R
  • CSU: Contacts of Structural Units for 2V4R
  • Likely Quarternary Molecular Structure file(s) for 2V4R
  • Structure Factors (94 Kb)
  • Retrieve 2V4R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V4R from S2C, [Save to disk]
  • Re-refined 2v4r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V4R 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 2V4R
  • 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 2V4R, from MSDmotif at EBI
  • Fold representative 2v4r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v4r_T] [2v4r_A] [2v4r_P] [2v4r]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2V4R
  • Community annotation for 2V4R 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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