3V9Z Hydrolase Dna date Dec 28, 2011
title Crystal Structure Of Rnase T In Complex With A Product Ssdna With One Mg In The Active Site
authors Y.Y.Hsiao, H.S.Yuan
compound source
Molecule: Ribonuclease T
Chain: A, B
Synonym: Exoribonuclease T, Rnase T
Ec: 3.1.13.-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ripl

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

Synthetic: Yes
Other_details: Synthetic Construct
symmetry Space Group: P 21 21 2
R_factor 0.211 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
96.422 106.092 46.952 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CO, MG enzyme Hydrolase E.C.3.1.13 BRENDA
A, B
  • nuclease activity
  • exonuclease activity
  • ribonuclease activity
  • 3'-5' exonuclease activity
  • exoribonuclease activity, pr...

  • Primary referenceHow an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes., Hsiao YY, Duh Y, Chen YP, Wang YT, Yuan HS, Nucleic Acids Res. 2012 Jun 19. PMID:22718982
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (3v9z.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 3V9Z
  • CSU: Contacts of Structural Units for 3V9Z
  • Structure Factors (336 Kb)
  • Retrieve 3V9Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V9Z from S2C, [Save to disk]
  • Re-refined 3v9z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V9Z in 3D
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  • Visual 3D analysis of 3V9Z
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3V9Z, from MSDmotif at EBI
  • Fold representative 3v9z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v9z_A] [3v9z] [3v9z_C] [3v9z_B] [3v9z_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3V9Z: [EXOIII ] by SMART
  • Other resources with information on 3V9Z
  • Community annotation for 3V9Z at PDBWiki (http://pdbwiki.org)
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