5I4A Rna Binding Protein Rna date Feb 11, 2016
title X-Ray Crystal Structure Of Marinitoga Piezophila Argonaute I With 5' Oh Guide Rna
authors K.W.Doxzen, E.Kaya, K.R.Knoll, R.C.Wilson, S.C.Strutt, P.J.Kranzu J.A.Doudna
compound source
Molecule: Argonaute Protein
Chain: A, C
Synonym: Mpago
Engineered: Yes
Organism_scientific: Marinitoga Piezophila (Strain Dsm 1428 11233 Ka3);
Organism_taxid: 443254
Strain: Dsm 14283 Jcm 11233 Ka3
Gene: Marpi_0405
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Rna (5'-R(Upapupapcpapapcpcpupapcpup
Chain: B, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.216 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.883 75.420 102.215 110.87 90.55 90.09
method X-Ray Diffractionresolution 1.95 Å
Gene MARPI
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceA bacterial Argonaute with noncanonical guide RNA specificity., Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA, Proc Natl Acad Sci U S A. 2016 Mar 30. pii: 201524385. PMID:27035975
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (486 Kb) [Save to disk]
  • Biological Unit Coordinates (5i4a.pdb1.gz) 237 Kb
  • Biological Unit Coordinates (5i4a.pdb2.gz) 239 Kb
  • CSU: Contacts of Structural Units for 5I4A
  • Structure Factors (6687 Kb)
  • Retrieve 5I4A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5I4A from S2C, [Save to disk]
  • Re-refined 5i4a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5I4A 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 5I4A
  • 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
  • Fold representative 5i4a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5i4a_C] [5i4a_B] [5i4a_A] [5i4a_D] [5i4a]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5I4A: [Piwi ] by SMART
  • Other resources with information on 5I4A
  • Community annotation for 5I4A at PDBWiki (http://pdbwiki.org)

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