3F2D Transferase Dna date Oct 29, 2008
title Dna Polymerase Polc From Geobacillus Kaustophilus Complex Wi Dgtp, Mn And Zn
authors D.R.Davies, R.J.Evans, J.M.Bullard, J.Christensen, L.S.Green, J.W W.K.Ribble, N.Janjic, T.C.Jarvis
compound source
Molecule: 5'-D(Dcpdapdgpdtpdgpdapdgpdapdcpdgpdgp Apdapdcpdc)-3';
Chain: P
Engineered: Yes
Other_details: Dna Primer Strand
Synthetic: Yes
Other_details: Primer Strand Is Synthetic Oligonucleotide

Molecule: 5'-D(Dapdtpdapdapdcpdgpdgpdtpdtpdgpdcp Gpdtpdcpdtpdcpdapdcpdtpdg)-3';
Chain: T
Engineered: Yes
Other_details: Dna Template Strand

Synthetic: Yes
Other_details: Template Strand Is Synthetic Oligonucleotide

Molecule: Geobacillus Kaustophilus Dna Polc
Chain: A
Fragment: Gkapolc, Delta 1-227, Delta 412-617
Engineered: Yes

Organism_scientific: Geobacillus Kaustophilus
Organism_taxid: 1462
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.216 R_Free 0.254
length a length b length c angle alpha angle beta angle gamma
115.997 139.479 184.074 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand DGT, MN, PO4, ZN enzyme Transferase E.C. BRENDA

Primary referenceStructure of PolC reveals unique DNA binding and fidelity determinants., Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC, Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20695-700. Epub 2008 Dec 23. PMID:19106298
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (3f2d.pdb1.gz) 172 Kb
  • LPC: Ligand-Protein Contacts for 3F2D
  • CSU: Contacts of Structural Units for 3F2D
  • Likely Quarternary Molecular Structure file(s) for 3F2D
  • Structure Factors (791 Kb)
  • Retrieve 3F2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F2D from S2C, [Save to disk]
  • Re-refined 3f2d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F2D 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 3F2D
  • 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 3F2D, from MSDmotif at EBI
  • Fold representative 3f2d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f2d_A] [3f2d_T] [3f2d] [3f2d_P]
  • SWISS-PROT database: [Q5L0J3]
  • Domain organization of [Q5L0J3_GEOKA] by SWISSPFAM
  • Domain found in 3F2D: [POLIIIAc ] by SMART
  • Other resources with information on 3F2D
  • Community annotation for 3F2D 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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