2G8F Hydrolase Rna Dna date Mar 02, 2006
title B. Halodurans Rnase H Catalytic Domain E188a Mutant In Compl Mg2+ And Rnadna Hybrid (Non-P Nick At The Active Site)
authors M.Nowotny, W.Yang
compound source
Molecule: 5'-R(Upcpgpapcpa)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Ribonuclease H
Chain: A
Fragment: Bh-Rnase Hc
Synonym: Rnase H
Ec: 3.1.26.4
Engineered: Yes
Mutation: Yes

Organism_scientific: Bacillus Halodurans
Organism_taxid: 86665
Gene: Rnha
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet15b
symmetry Space Group: C 1 2 1
R_factor 0.182 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.072 36.858 61.796 90.00 96.47 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand CL, MG enzyme Hydrolase E.C.3.1.26.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release., Nowotny M, Yang W, EMBO J. 2006 May 3;25(9):1924-33. Epub 2006 Apr 6. PMID:16601679
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (2g8f.pdb1.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 2G8F
  • CSU: Contacts of Structural Units for 2G8F
  • Likely Quarternary Molecular Structure file(s) for 2G8F
  • Structure Factors (321 Kb)
  • Retrieve 2G8F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2G8F from S2C, [Save to disk]
  • Re-refined 2g8f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2G8F 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 2G8F
  • 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 2G8F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2g8f] [2g8f_C] [2g8f_B] [2g8f_A]
  • SWISS-PROT database: [Q9KEI9]
  • Domain organization of [RNH1_BACHD] by SWISSPFAM
  • Other resources with information on 2G8F
  • Community annotation for 2G8F 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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