1LV5 Transferase Dna date May 24, 2002
title Crystal Structure Of The Closed Conformation Of Bacillus Dna Polymerase I Fragment Bound To Dna And Dctp
authors S.J.Johnson, J.S.Taylor, L.S.Beese
compound source
Molecule: 5'-D(Gpgpaptpcpapgpcpgpa)-3'
Chain: C, E
Engineered: Yes
Other_details: Primer Strand
Synthetic: Yes

Molecule: 5'-D(Apcpgptpcpgpcptpgpaptpcpcpg)- 3';
Chain: D, F
Engineered: Yes
Other_details: Template Strand

Synthetic: Yes

Molecule: Dna Polymerase I
Chain: A, B
Fragment: Bacillus Fragment (Analogous To The E. Coli Klenow Fragment);
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-30a(+)
Other_details: This Protein Was Isolated From An As Yet Unnamed Novel Strain Of Bacillus Stearothermophilus (See Ref 2).
symmetry Space Group: P 31
R_factor 0.218 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.681 91.681 190.116 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.95 Å
ligand DCP, MG, MN, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1L5U, 1NKB
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceProcessive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations., Johnson SJ, Taylor JS, Beese LS, Proc Natl Acad Sci U S A 2003 Apr 1;100(7):3895-900. PMID:12649320
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (218 Kb) [Save to disk]
  • Biological Unit Coordinates (1lv5.pdb1.gz) 108 Kb
  • Biological Unit Coordinates (1lv5.pdb2.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 1LV5
  • CSU: Contacts of Structural Units for 1LV5
  • Likely Quarternary Molecular Structure file(s) for 1LV5
  • Structure Factors (1091 Kb)
  • Retrieve 1LV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LV5 from S2C, [Save to disk]
  • Re-refined 1lv5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LV5 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 1LV5
  • 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 1LV5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lv5a1, region A:297-468 [Jmol] [rasmolscript] [script source]
        - Domain d1lv5a2, region A:469-876 [Jmol] [rasmolscript] [script source]
        - Domain d1lv5b1, region B:297-468 [Jmol] [rasmolscript] [script source]
        - Domain d1lv5b2, region B:469-876 [Jmol] [rasmolscript] [script source]
  • Fold representative 1lv5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1lv5_A] [1lv5] [1lv5_B] [1lv5_F] [1lv5_E] [1lv5_C] [1lv5_D]
  • SWISS-PROT database: [P52026]
  • Domain organization of [DPO1_BACST] by SWISSPFAM
  • Domains found in 1LV5: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 1LV5
  • Community annotation for 1LV5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science