3V6K Transferase Dna date Dec 20, 2011
title Replication Of N2,3-Ethenoguanine By Dna Polymerases
authors L.Zhao
compound source
Molecule: Dna Polymerase Iv
Chain: A, J
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus P2
Organism_taxid: 273057
Strain: Atcc 35092 Dsm 1617 Jcm 11322 P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Gold (De3)
Expression_system_vector_type: Plasmid

Molecule: Dna (5'-D(Pgpapapgpgpaptptpcp(2dt))-3')
Chain: P, K
Engineered: Yes
Other_details: Primer

Synthetic: Yes
Other_details: Based On Previously Crystallization Sequence

Molecule: Dna (5'-D(Tpcpapcp(Efg)Pgpapaptpcpcpt 3');
Chain: B, M
Engineered: Yes
Other_details: Template

Synthetic: Yes
Other_details: Based On Previously Crystallization Sequence
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.303
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.855 110.953 100.238 90.00 102.70 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand 2DT, CA, EFG, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, J


Primary referenceReplication of N(2) ,3-Ethenoguanine by DNA Polymerases., Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP, Angew Chem Int Ed Engl. 2012 Apr 4. doi: 10.1002/anie.201109004. PMID:22488769
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (271 Kb) [Save to disk]
  • Biological Unit Coordinates (3v6k.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (3v6k.pdb2.gz) 126 Kb
  • LPC: Ligand-Protein Contacts for 3V6K
  • CSU: Contacts of Structural Units for 3V6K
  • Structure Factors (196 Kb)
  • Retrieve 3V6K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V6K from S2C, [Save to disk]
  • Re-refined 3v6k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V6K 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 3V6K
  • 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 3V6K, from MSDmotif at EBI
  • Fold representative 3v6k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v6k_K] [3v6k_M] [3v6k] [3v6k_J] [3v6k_A] [3v6k_P] [3v6k_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3V6K
  • Community annotation for 3V6K at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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