4OI0 Rna Binding Protein Rna date Jan 18, 2014
title Bound To Ssrna Dinucleotide Gc, Adp, Alf4-, And Mg2+(Transit Data Set I)
authors A.Dikfidan, B.Loll, C.Zeymer, T.Clausen, A.Meinhart
compound source
Molecule: Protein Clpf-1
Chain: A
Engineered: Yes
Organism_scientific: Caenorhabditis Elegans
Organism_common: Nematode
Organism_taxid: 6239
Gene: Clpf-1, F59a2.4
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Rna (5'-R(Gpc)-3')
Chain: B
Engineered: Yes
Other_details: Diribonucleotide Gc

Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: P 31
R_factor 0.227 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.710 100.710 40.400 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand 2PE, ADP, ALF, MG, SAR enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1., Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A, Mol Cell. 2014 Jun 19;54(6):975-86. doi: 10.1016/j.molcel.2014.04.005. Epub 2014 , May 8. PMID:24813946
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (4oi0.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 4OI0
  • CSU: Contacts of Structural Units for 4OI0
  • Structure Factors (428 Kb)
  • Retrieve 4OI0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OI0 from S2C, [Save to disk]
  • Re-refined 4oi0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OI0 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 4OI0
  • 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 4OI0, from MSDmotif at EBI
  • Fold representative 4oi0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4oi0_B] [4oi0_A] [4oi0]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4OI0
  • Community annotation for 4OI0 at PDBWiki (http://pdbwiki.org)

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