3CTR Hydrolase date Apr 14, 2008
title Crystal Structure Of The Rrm-Domain Of The Poly(A)-Specific Ribonuclease Parn Bound To M7gtp
authors T.Monecke, S.Schell, A.Dickmanns, R.Ficner
compound source
Molecule: Poly(A)-Specific Ribonuclease Parn
Chain: A
Fragment: Rna-Recognition-Motif Of Parn (Residues 445-540)
Synonym: Polyadenylate-Specific Ribonuclease, Deadenylating Deadenylation Nuclease;
Ec: 3.1.13.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Parn, Dan
Expression_system: Escherichia Coli
Expression_system_strain: Bl 21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-Parn3
symmetry Space Group: I 41 2 2
R_factor 0.210 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.107 81.107 78.058 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand MGP enzyme Hydrolase E.C.3.1.13.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode., Monecke T, Schell S, Dickmanns A, Ficner R, J Mol Biol. 2008 Oct 17;382(4):827-34. Epub 2008 Jul 31. PMID:18694759
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (20 Kb) [Save to disk]
  • Biological Unit Coordinates (3ctr.pdb1.gz) 15 Kb
  • Biological Unit Coordinates (3ctr.pdb2.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 3CTR
  • CSU: Contacts of Structural Units for 3CTR
  • Likely Quarternary Molecular Structure file(s) for 3CTR
  • Structure Factors (115 Kb)
  • Retrieve 3CTR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CTR from S2C, [Save to disk]
  • Re-refined 3ctr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CTR 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 3CTR
  • 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 3CTR, from MSDmotif at EBI
  • Fold representative 3ctr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ctr_A] [3ctr]
  • SWISS-PROT database: [O95453]
  • Domain organization of [PARN_HUMAN] by SWISSPFAM
  • Other resources with information on 3CTR
  • Community annotation for 3CTR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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