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
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

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.

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