1Q3B Hydrolase date Jul 29, 2003
title Crystal Structure Of The Dna Repair Enzyme Endonuclease-Viii From E. Coli: The R252a Mutant At 2.05 Resolution.
authors G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.K A.P.Grollman, G.Shoham
compound source
Molecule: Endonuclease Viii
Chain: A
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Nei
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet13a
symmetry Space Group: I 2 2 2
R_factor 0.228 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.722 80.051 169.311 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand GOL, MG, ZN enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 1K3W, 1Q3C
Gene
Ontology
ChainFunctionProcessComponent
A
  • endonuclease activity


  • Primary referenceStructure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility., Golan G, Zharkov DO, Feinberg H, Fernandes AS, Zaika EI, Kycia JH, Grollman AP, Shoham G, Nucleic Acids Res 2005 Sep 6;33(15):5006-16. Print 2005. PMID:16145054
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1q3b.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1Q3B
  • CSU: Contacts of Structural Units for 1Q3B
  • Likely Quarternary Molecular Structure file(s) for 1Q3B
  • Retrieve 1Q3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q3B from S2C, [Save to disk]
  • View 1Q3B 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 1Q3B
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1Q3B, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q3ba2, region A:1-124 [Jmol] [rasmolscript] [script source]
        - Domain d1q3ba1, region A:125-213 [Jmol] [rasmolscript] [script source]
        - Domain d1q3ba3, region A:217-262 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1q3b] [1q3b_A]
  • SWISS-PROT database: [P50465]
  • Domain organization of [END8_ECOLI] by SWISSPFAM
  • Domains found in 1Q3B: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1Q3B
  • Community annotation for 1Q3B 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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