1YTU

Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

Structural Biology Knowledgebase: 1YTU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YTU

Classification: RNA binding Protein / RNA

Total Structure Weight: 105998.41


Macromolecule Entities
Molecule Chains Length Organism Details
hypothetical protein AF1318 A, B 427 Archaeoglobus fulgidus Mutation: M1M, M2M, M112M, M139M, M200M, M208M, M260M, M280M, M301M, M339M, M377M
Gene Name(s): AF_1318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(P*AP*GP*AP*CP*AP*G)-3' C, E 6 synthetic
5'-R(P*UP*GP*UP*C)-3' D, F 4 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.204
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 238.75 α = 90.00
b = 238.75 β = 90.00
c = 52.04 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-11
  • Released Date: 2005-04-05
  • Deposition author(s): Ma, J.B., Yuan, Y.R., Meister, G., Pei, Y., Tuschl, T., Patel, D.J.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4