2AGP Transferase Dna date Jul 27, 2005
title Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection Pyrophosphorolysis
authors H.Ling, W.Yang
compound source
Molecule: Dna (5'-D(Gpgpgpgpgpapapgpgpaptptp(D
Chain: C, E
Engineered: Yes
Synthetic: Yes
Other_details: Chemically Synthesized

Molecule: Dna (5'- D(Tptptptpgpapaptpcpcptptpcpcpcpcpc)-3');
Chain: D, F
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized

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

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dbh, Dpo4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.867 101.463 105.642 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CA, DGT, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceFidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis., Vaisman A, Ling H, Woodgate R, Yang W, EMBO J 2005 Sep 7;24(17):2957-67. Epub 2005 Aug 18. PMID:16107880
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (2agp.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (2agp.pdb2.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 2AGP
  • CSU: Contacts of Structural Units for 2AGP
  • Likely Quarternary Molecular Structure file(s) for 2AGP
  • Structure Factors (166 Kb)
  • Retrieve 2AGP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2AGP from S2C, [Save to disk]
  • Re-refined 2agp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2AGP 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 2AGP
  • 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 2AGP, from MSDmotif at EBI
  • Fold representative 2agp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2agp_A] [2agp_E] [2agp_F] [2agp] [2agp_B] [2agp_C] [2agp_D]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2AGP
  • Community annotation for 2AGP 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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