3A4Y Hydrolase date Jul 22, 2009
title Crystal Structure Of H61a Mutant Ttha0252 From Thermus Therm Hb8
authors H.Ishikawa, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui, Riken S Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Ribonuclease Ttha0252
Chain: A, B, C, D
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Ttha0252
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: C 1 2 1
R_factor 0.239 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
143.144 146.767 121.123 90.00 109.24 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand FLC, SO4, ZN enzyme Hydrolase E.C.3.1 BRENDA
note 3A4Y supersedes 2ZDW
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • nuclease activity
  • endonuclease activity


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (284 Kb) [Save to disk]
  • Biological Unit Coordinates (3a4y.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (3a4y.pdb2.gz) 74 Kb
  • Biological Unit Coordinates (3a4y.pdb3.gz) 74 Kb
  • Biological Unit Coordinates (3a4y.pdb4.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3A4Y
  • CSU: Contacts of Structural Units for 3A4Y
  • Structure Factors (1021 Kb)
  • Retrieve 3A4Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A4Y from S2C, [Save to disk]
  • Re-refined 3a4y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A4Y 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 3A4Y
  • 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 3A4Y, from MSDmotif at EBI
  • Fold representative 3a4y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a4y_D] [3a4y] [3a4y_C] [3a4y_B] [3a4y_A]
  • SWISS-PROT database: [Q5SLP1]
  • Domain organization of [RNSE_THET8] by SWISSPFAM
  • Domains found in 3A4Y: [Beta-Casp] [Lactamase_B ] by SMART
  • Other resources with information on 3A4Y
  • Community annotation for 3A4Y 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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