4OI1 Rna Binding Protein Rna date Jan 18, 2014
title Clp1 Bound To Ssrna Dinucleotide Gc, Adp, Alf4-, And Mg2+(Tr State, Data Set II)
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 0.190 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
100.740 100.740 40.410 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 2PE, ADP, ALF, MG enzyme

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] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (4oi1.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 4OI1
  • CSU: Contacts of Structural Units for 4OI1
  • Structure Factors (381 Kb)
  • Retrieve 4OI1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OI1 from S2C, [Save to disk]
  • Re-refined 4oi1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OI1 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 4OI1
  • 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 4OI1, from MSDmotif at EBI
  • Fold representative 4oi1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4oi1_B] [4oi1_A] [4oi1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4OI1
  • Community annotation for 4OI1 at PDBWiki (http://pdbwiki.org)

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