3O3F Hydrolase Dna-Rna Hybrid date Jul 24, 2010
title T. Maritima Rnase H2 D107n In Complex With Nucleic Acid Subs Magnesium Ions
authors M.P.Rychlik, H.Chon, S.M.Cerritelli, P.Klimek, R.J.Crouch, M.Nowo
compound source
Molecule: Ribonuclease Hii
Chain: A
Synonym: Rnase Hii
Ec: 3.1.26.4
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336
Gene: Rnhb, Tm_0915
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21

Molecule: Dna (5'-D(Gpapaptpcpapgpgptpgptpc)-3'
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Dnarna (5'-D(Gpapcpapc)-R(Pc)-D(Ptpgpap 3');
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.191 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.062 48.570 78.391 90.00 131.80 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MG enzyme Hydrolase E.C.3.1.26.4 BRENDA
Gene TM
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • RNA-DNA hybrid ribonuclease ...


  • Primary referenceCrystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage., Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M, Mol Cell. 2010 Nov 24;40(4):658-70. PMID:21095591
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (3o3f.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 3O3F
  • CSU: Contacts of Structural Units for 3O3F
  • Structure Factors (322 Kb)
  • Retrieve 3O3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O3F from S2C, [Save to disk]
  • Re-refined 3o3f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O3F 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 3O3F
  • 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 3O3F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o3f_C] [3o3f_D] [3o3f_A] [3o3f]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3O3F
  • Community annotation for 3O3F 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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