3EZ5 Transferase Dna date Oct 22, 2008
title Cocrystal Structure Of Bacillus Fragment Dna Polymerase I Wi Dna , Dctp, And Zinc (Closed Form).
authors J.J.Warren, E.Y.Wu, A.A.Golosov, M.Karplus, L.S.Beese
compound source
Molecule: Dna Polymerase I
Chain: A, D
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Bacillus Stearothermophilus
Gene: Pola
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc

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

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.551 108.572 149.756 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand DAD, FRU, GLC, SO4, ZN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceThe mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis., Golosov AA, Warren JJ, Beese LS, Karplus M, Structure. 2010 Jan 13;18(1):83-93. PMID:20152155
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk]
  • Biological Unit Coordinates (3ez5.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (3ez5.pdb2.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 3EZ5
  • CSU: Contacts of Structural Units for 3EZ5
  • Structure Factors (1761 Kb)
  • Retrieve 3EZ5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EZ5 from S2C, [Save to disk]
  • Re-refined 3ez5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EZ5 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 3EZ5
  • 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
  • 3D motif for 3EZ5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ez5_E] [3ez5_F] [3ez5_B] [3ez5_A] [3ez5_D] [3ez5] [3ez5_C]
  • SWISS-PROT database: [P52026]
  • Domain organization of [DPO1_BACST] by SWISSPFAM
  • Domains found in 3EZ5: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 3EZ5
  • Community annotation for 3EZ5 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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