3VJR Hydrolase Rna date Oct 28, 2011
title Crystal Structure Of Peptidyl-Trna Hydrolase From Escherichi Complex With The Cca-Acceptor-T[Psi]C Domain Of Trna
authors K.Ito, R.Murakami, M.Mochizuki, H.Qi, Y.Shimizu, K.I.Miura, T.Ueda T.Uchiumi
compound source
Molecule: Peptidyl-Trna Hydrolase
Chain: A, C
Synonym: Pth
Ec: 3.1.1.29
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Pth, B1204, Jw1195
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Trna Cca-Acceptor
Chain: B, D
Engineered: Yes

Synthetic: Yes
Other_details: Rna Was Repeated By In Vitro Transcription
symmetry Space Group: P 61
R_factor 0.193 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.070 55.070 413.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand
enzyme Hydrolase E.C.3.1.1.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase., Ito K, Murakami R, Mochizuki M, Qi H, Shimizu Y, Miura KI, Ueda T, Uchiumi T, Nucleic Acids Res. 2012 Aug 25. PMID:22923517
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (3vjr.pdb1.gz) 186 Kb
  • CSU: Contacts of Structural Units for 3VJR
  • Structure Factors (408 Kb)
  • Retrieve 3VJR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VJR from S2C, [Save to disk]
  • Re-refined 3vjr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VJR 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 3VJR
  • 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 3VJR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vjr_C] [3vjr_B] [3vjr] [3vjr_A] [3vjr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VJR
  • Community annotation for 3VJR at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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