1U48 Transferase Dna date Jul 23, 2004
title Extension Of A Cytosine-8-Oxoguanine Base Pair
authors G.W.Hsu, M.Ober, T.Carell, L.S.Beese
compound source
Molecule: Dna Primer Strand
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna Template Strand With 8-Oxoguanine
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase I
Chain: A
Fragment: Analogous To The E. Coli Klenow Fragment
Synonym: Pol I
Ec: 2.7.7.7
Engineered: Yes
Other_details: See Remark 400

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(+)
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.342 93.265 106.084 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 8OG, FRU, GLC, MG, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1NK5, 1UA0
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceError-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase., Hsu GW, Ober M, Carell T, Beese LS, Nature. 2004 Sep 9;431(7005):217-21. Epub 2004 Aug 22. PMID:15322558
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (1u48.pdb1.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 1U48
  • CSU: Contacts of Structural Units for 1U48
  • Likely Quarternary Molecular Structure file(s) for 1U48
  • Structure Factors (603 Kb)
  • Retrieve 1U48 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U48 from S2C, [Save to disk]
  • Re-refined 1u48 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1U48 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 1U48
  • 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 1U48, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u48a1, region A:299-468 [Jmol] [rasmolscript] [script source]
        - Domain d1u48a2, region A:469-876 [Jmol] [rasmolscript] [script source]
  • Fold representative 1u48 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: [1u48_C] [1u48_B] [1u48_A] [1u48]
  • SWISS-PROT database: [P52026]
  • Domain organization of [DPO1_BACST] by SWISSPFAM
  • Domains found in 1U48: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 1U48
  • Community annotation for 1U48 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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