5DIZ Hydrolase date Sep 01, 2015
title Crystal Structure Of Nuclear Proteinaceous Rnase P 2 (Prorp2 Thaliana
authors A.Karasik, A.Shanmuganathan, M.J.Howard, C.A.Fierke, M.Koutmos
compound source
Molecule: Proteinaceous Rnase P 2
Chain: A, B
Ec: 3.1.26.5
Engineered: Yes
Organism_scientific: Arabidopsis Thaliana
Organism_common: Mouse-Ear Cress
Organism_taxid: 3702
Gene: Prorp2, At2g16650, T24i21.6
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pmcsg7
symmetry Space Group: P 1
R_factor 0.228 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.980 76.993 80.112 72.66 64.11 77.76
method X-Ray Diffractionresolution 3.20 Å
ligand ZN enzyme Hydrolase E.C.3.1.26.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • ribonuclease P activity


  • Primary referenceNuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes., Karasik A, Shanmuganathan A, Howard MJ, Fierke CA, Koutmos M, J Mol Biol. 2015 Dec 3. pii: S0022-2836(15)00687-7. doi:, 10.1016/j.jmb.2015.11.025. PMID:26655022
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (286 Kb) [Save to disk]
  • Biological Unit Coordinates (5diz.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (5diz.pdb2.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 5DIZ
  • CSU: Contacts of Structural Units for 5DIZ
  • Structure Factors (351 Kb)
  • Retrieve 5DIZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DIZ from S2C, [Save to disk]
  • Re-refined 5diz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DIZ 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 5DIZ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5diz] [5diz_A] [5diz_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DIZ
  • Community annotation for 5DIZ at PDBWiki (http://pdbwiki.org)

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