2W9A Transferase Dna date Jan 22, 2009
title Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl- Deoxyguanosine Modified Dna With Incoming Dgtp
authors R.L.Eoff, H.Zhang, I.D.Kosekov, C.J.Rizzo, M.Egli, F.P.Guengerich
compound source
Molecule: Dna Polymerase Iv
Chain: A
Synonym: Pol Iv, Dpo4
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
Synonym: Primer Dna
Other_details: 14 Base Primer Dna 5'-Ggg Gga Agg Att C(Doc) -3';

Synthetic: Yes

Molecule: 5'-D(Tpcpapcpo2gpgpapaptpcp Cptptpcpcpcpcpc)-3';
Chain: T
Synonym: Template Dna
Other_details: 18 Base Template Dna 5'-Tca C(O2g)G Aat Cct Tcc Ccc-3'

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.213 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.670 103.757 52.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand DGT, DOC, MG, O2G enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES., Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP, J Biol Chem. 2009 Jun 26;284(26):17687-99. PMID:19542237
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2w9a.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 2W9A
  • CSU: Contacts of Structural Units for 2W9A
  • Likely Quarternary Molecular Structure file(s) for 2W9A
  • Structure Factors (85 Kb)
  • Retrieve 2W9A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W9A from S2C, [Save to disk]
  • Re-refined 2w9a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W9A 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 2W9A
  • 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 2W9A, from MSDmotif at EBI
  • Fold representative 2w9a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w9a_P] [2w9a] [2w9a_A] [2w9a_T]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2W9A
  • Community annotation for 2W9A 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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