4DSE Transferase Dna date Feb 18, 2012
title Ternary Complex Of Bacillus Dna Polymerase I Large Fragment Duplex, And Rctp (Paired With Dg Of Template) In Presence O
authors W.Wang, L.S.Beese
compound source
Molecule: Dna Polymerase
Chain: A, D
Fragment: Unp Residues 287-878
Engineered: Yes
Mutation: Yes
Organism_scientific: Geobacillus Kaustophilus
Organism_taxid: 235909
Strain: Hta426
Gene: Pola, Gk2730
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30a

Molecule: Dna (5'-D(Cpcptpgpapcptpcp(Doc))-3')
Chain: B, E
Engineered: Yes
Other_details: Dna Primer Strand

Synthetic: Yes

Molecule: Dna (5'-D(Cpaptpgpgpgpapgptpcpapgpg)
Chain: C, F
Engineered: Yes
Other_details: Dna Template Strand

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.175 R_Free 0.200
length a length b length c angle alpha angle beta angle gamma
93.850 109.510 150.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.67 Å
ligand CTP, DOC, SO4 enzyme Transferase E.C. BRENDA
A, D

Primary referenceStructural factors that determine selectivity of a high-fidelity DNA polymerase for deoxy-, dideoxy-, and ribo-nucleotides., Wang W, Wu EY, Hellinga HW, Beese LS, J Biol Chem. 2012 May 30. PMID:22648417
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (637 Kb) [Save to disk]
  • Biological Unit Coordinates (4dse.pdb1.gz) 303 Kb
  • Biological Unit Coordinates (4dse.pdb2.gz) 327 Kb
  • LPC: Ligand-Protein Contacts for 4DSE
  • CSU: Contacts of Structural Units for 4DSE
  • Structure Factors (1168 Kb)
  • Retrieve 4DSE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DSE from S2C, [Save to disk]
  • Re-refined 4dse structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DSE 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 4DSE
  • 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 4DSE, from MSDmotif at EBI
  • Fold representative 4dse from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dse_D] [4dse_E] [4dse_F] [4dse] [4dse_A] [4dse_C] [4dse_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DSE: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4DSE
  • Community annotation for 4DSE at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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