3I5Y Hydrolase Rna date Jul 06, 2009
title Structure Of Mss116p Bound To Ssrna Containing A Single 5-Br Pnp
authors M.Del Campo, A.M.Lambowitz
compound source
Molecule: Atp-Dependent Rna Helicase Mss116
Chain: A
Fragment: Unp Residues 37 To 597
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Gene: Mss116, Yd9346.05c, Ydr194c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal

Molecule: 5'-R(Upupup(5bu)Pupupupupupu)-3'
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Rna Fragment Commercially Available
symmetry Space Group: P 21 21 2
R_factor 0.204 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.190 126.352 55.990 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand 5BU, ANP, MG enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA., Del Campo M, Lambowitz AM, Mol Cell. 2009 Sep 11;35(5):598-609. PMID:19748356
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (3i5y.pdb1.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 3I5Y
  • CSU: Contacts of Structural Units for 3I5Y
  • Structure Factors (330 Kb)
  • Retrieve 3I5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I5Y from S2C, [Save to disk]
  • Re-refined 3i5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3I5Y 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 3I5Y
  • 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 3I5Y, from MSDmotif at EBI
  • Fold representative 3i5y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i5y_A] [3i5y_B] [3i5y]
  • SWISS-PROT database: [P15424]
  • Domain organization of [MS116_YEAST] by SWISSPFAM
  • Domains found in 3I5Y: [DEXDc] [HELICc ] by SMART
  • Other resources with information on 3I5Y
  • Community annotation for 3I5Y at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science