2O6M Hydrolase Dna date Dec 07, 2006
title H98q Mutant Of The Homing Endonuclease I-Ppoi Complexed With
authors J.H.Eastberg, B.L.Stoddard
compound source
Molecule: 5'-D(Dtpdtpdgpdapdcpdtpdcpdtpdcpdtpdtp Gpdapdgpdapdgpdtpdcpda)-3';
Chain: C, D
Engineered: Yes
Other_details: I-Ppoi Binding Sequence
Synthetic: Yes

Molecule: Intron-Encoded Endonuclease I-Ppoi
Chain: A, B
Synonym: I-Ppo
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Physarum Polycephalum
Organism_taxid: 5791
Gene: I-Ppoi
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Ppo
symmetry Space Group: P 31 2 1
R_factor 0.211 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.850 113.850 88.880 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand MG, ZN enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceMutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism., Eastberg JH, Eklund J, Monnat R Jr, Stoddard BL, Biochemistry. 2007 Jun 19;46(24):7215-25. Epub 2007 May 22. PMID:17516660
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (2o6m.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 2O6M
  • CSU: Contacts of Structural Units for 2O6M
  • Likely Quarternary Molecular Structure file(s) for 2O6M
  • Structure Factors (357 Kb)
  • Retrieve 2O6M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O6M from S2C, [Save to disk]
  • Re-refined 2o6m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2O6M 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 2O6M
  • 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 2O6M, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o6m_A] [2o6m] [2o6m_B] [2o6m_D] [2o6m_C]
  • SWISS-PROT database: [Q94702]
  • Domain organization of [PPO1_PHYPO] by SWISSPFAM
  • Other resources with information on 2O6M
  • Community annotation for 2O6M 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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