4DSI Transferase Dna date Feb 19, 2012
title Crystal Structure Of Fragment Dna Polymerase I From Bacillus Stearothermophilus With Duplex Dna, Se-Dgtp And Calcium
authors J.H.Gan, R.Abdur, H.H.Liu, J.Sheng, J.Caton-Willians, A.S.Soares,
compound source
Molecule: Dna Polymerase
Chain: A
Fragment: Residues 298-876
Engineered: Yes
Mutation: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Dpo1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: Dna
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Dna

Molecule: Se-Dgtp
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Se-Modified Dgtp
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.234
length a length b length c angle alpha angle beta angle gamma
88.573 93.387 105.928 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand CA, DG, GOL, SO4 enzyme Transferase E.C. BRENDA
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity

  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (4dsi.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 4DSI
  • CSU: Contacts of Structural Units for 4DSI
  • Structure Factors (1207 Kb)
  • Retrieve 4DSI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DSI from S2C, [Save to disk]
  • Re-refined 4dsi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DSI 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 4DSI
  • 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 4DSI, from MSDmotif at EBI
  • Fold representative 4dsi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dsi] [4dsi_B] [4dsi_C] [4dsi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DSI: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4DSI
  • Community annotation for 4DSI at PDBWiki (http://pdbwiki.org)

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