4X4R Rna Binding Protein date Dec 03, 2014
title Crystal Structure Of The A.Fulgidus Cca-Adding Enzyme In Com A G70a Arginyl-Trna Minihelix Ending In Ccacc And Ampcpp
authors C.D.Kuhn, L.Joshua-Tor
compound source
Molecule: Cca-Adding Enzyme
Chain: A, C
Fragment: A. Fulgidus Cca-Adding Enzyme
Synonym: Cca Trna Nucleotidyltransferase,Trna Cca-Pyrophosp Trna Adenylyl-Cytidylyl- Transferase,Trna Nucleotidyltrans Trna-Nt;
Ec: 2.7.7.72
Engineered: Yes
Organism_scientific: Archaeoglobus Fulgidus
Organism_taxid: 224325
Strain: Atcc 49558 Vc-16 Dsm 4304 Jcm 9628 Nbrc 100
Gene: Cca, Af_2156
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22

Molecule: G70a Trna Minihelix Ending In Ccacc
Chain: B, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Rna (5'-D(Cpg)-3')
Chain: H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.209 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.100 217.368 58.562 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand APC, GOL, MES, MG, PEG, TAR enzyme Transferase E.C.2.7.7.72 BRENDA
Gene AF
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceOn-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme., Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L, Cell. 2015 Feb 12;160(4):644-58. doi: 10.1016/j.cell.2015.01.005. Epub 2015 Jan, 29. PMID:25640237
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (340 Kb) [Save to disk]
  • Biological Unit Coordinates (4x4r.pdb1.gz) 170 Kb
  • Biological Unit Coordinates (4x4r.pdb2.gz) 166 Kb
  • LPC: Ligand-Protein Contacts for 4X4R
  • CSU: Contacts of Structural Units for 4X4R
  • Structure Factors (543 Kb)
  • Retrieve 4X4R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4X4R from S2C, [Save to disk]
  • Re-refined 4x4r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4X4R 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 4X4R
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4X4R, from MSDmotif at EBI
  • Fold representative 4x4r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4x4r_D] [4x4r_C] [4x4r_H] [4x4r_B] [4x4r] [4x4r_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4X4R
  • Community annotation for 4X4R at PDBWiki (http://pdbwiki.org)

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