3TFR Transferase Dna date Aug 16, 2011
title Ternary Complex Structure Of Dna Polymerase Beta With A Gapp Substrate And A, B Damp(Cf2)Pp In The Active Site
authors B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: Dna (5'-D(Cpcpgpapcptpgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.890 79.380 55.650 90.00 107.64 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CL, F3A, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStereospecific Formation of a Ternary Complex of (S)-alpha,beta-Fluoromethylene-dATP with DNA Pol beta., Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH, Chembiochem. 2012 Mar 5;13(4):528-30. doi: 10.1002/cbic.201100738. Epub 2012 Feb , 7. PMID:22315190
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3tfr.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 3TFR
  • CSU: Contacts of Structural Units for 3TFR
  • Structure Factors (398 Kb)
  • Retrieve 3TFR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TFR from S2C, [Save to disk]
  • Re-refined 3tfr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3TFR 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 3TFR
  • 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 3TFR, from MSDmotif at EBI
  • Fold representative 3tfr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tfr_A] [3tfr] [3tfr_D] [3tfr_T] [3tfr_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3TFR: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3TFR
  • Community annotation for 3TFR at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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