4DSL Transferase Dna date Feb 19, 2012
title Crystal Structure Of Fragment Dna Polymerase I From Bacillus Stearothermophilus With Duplex Dna 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
Ec: 2.7.7.7
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 (5'-D(Ggpcptpapcpapgpgpapcptpc)-
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Dna

Molecule: Dna (5'- D(Tpcpapcpgpapgptpcpcptpgptpapgpcpc)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Dna
symmetry Space Group: P 21 21 21
R_factor 0.222 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.340 93.587 104.618 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (4dsl.pdb1.gz) 206 Kb
  • LPC: Ligand-Protein Contacts for 4DSL
  • CSU: Contacts of Structural Units for 4DSL
  • Structure Factors (695 Kb)
  • Retrieve 4DSL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DSL from S2C, [Save to disk]
  • Re-refined 4dsl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DSL 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 4DSL
  • 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 4DSL, from MSDmotif at EBI
  • Fold representative 4dsl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dsl_B] [4dsl] [4dsl_C] [4dsl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DSL: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 4DSL
  • Community annotation for 4DSL at PDBWiki (http://pdbwiki.org)

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