2V9W Transferase date Aug 27, 2007
title Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide In The Template Strand
authors A.Irimia, P.S.Pallan, M.Egli
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Other_details: Dpo4
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: Pet22b-Dpo4-Nhis

Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Cptpg)-3'
Chain: C, E
Other_details: 13-Mer Primer

Synthetic: Yes

Molecule: 5'-D(Tptpcpapgpdftpapgptpcpcp Tptpcpcpcpcpc)-3';
Chain: D, F
Other_details: 18-Mer Template

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.704 186.744 52.730 90.00 110.06 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CA, DCT, DFT enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure and Activity of Y-class DNA Polymerase DPO4 from Sulfolobus solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene., Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M, J Biol Chem. 2007 Dec 14;282(50):36421-33. Epub 2007 Oct 18. PMID:17951245
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (2v9w.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (2v9w.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 2V9W
  • CSU: Contacts of Structural Units for 2V9W
  • Likely Quarternary Molecular Structure file(s) for 2V9W
  • Structure Factors (129 Kb)
  • Retrieve 2V9W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V9W from S2C, [Save to disk]
  • Re-refined 2v9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V9W 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 2V9W
  • 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 2V9W, from MSDmotif at EBI
  • Fold representative 2v9w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v9w_A] [2v9w_F] [2v9w_C] [2v9w] [2v9w_D] [2v9w_B] [2v9w_E]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2V9W
  • Community annotation for 2V9W 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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