2JEF Transferase Dna date Jan 17, 2007
title The Molecular Basis Of Selectivity Of Nucleotide Triphosphat Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfa Dna Polymerase Iv: Steady-State And Pre-Steady-State And X- Crystallography Of Correct And Incorrect Pairing
authors R.L.Eoff, K.C.Angel, I.D.Kosekov, M.Egli, F.P.Guengerich
compound source
Molecule: Dna Polymerase Iv
Chain: A
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Other_details: His-Tag Added To N-Terminus
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet22bdpo4-Nhis

Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptptpcpdoc)
Chain: P
Engineered: Yes
Other_details: Doc Indicates A Dideoxy-Cytosine Residue

Synthetic: Yes

Molecule: 5'-D(Tpcpapcpbzgpgpapaptpcpcptptpcp Cpcpc)-3';
Chain: T
Engineered: Yes
Other_details: Bzg Indicates O6-Benzylguanine Modification

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.230 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.990 102.660 52.880 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.17 Å
ligand BZG, CA, DGT, DOC enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular basis of selectivity of nucleoside triphosphate incorporation opposite O6-benzylguanine by sulfolobus solfataricus DNA polymerase Dpo4: steady-state and pre-steady-state kinetics and x-ray crystallography of correct and incorrect pairing., Eoff RL, Angel KC, Egli M, Guengerich FP, J Biol Chem. 2007 May 4;282(18):13573-84. Epub 2007 Mar 3. PMID:17337730
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (2jef.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2JEF
  • CSU: Contacts of Structural Units for 2JEF
  • Likely Quarternary Molecular Structure file(s) for 2JEF
  • Structure Factors (132 Kb)
  • Retrieve 2JEF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JEF from S2C, [Save to disk]
  • Re-refined 2jef structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2JEF 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 2JEF
  • 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 2JEF, from MSDmotif at EBI
  • Fold representative 2jef from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2jef] [2jef_T] [2jef_P] [2jef_A]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2JEF
  • Community annotation for 2JEF 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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