3NVI Transferase Rna date Jul 08, 2010
title Structure Of N-Terminal Truncated Nop5658 Bound With L7ae A Rna
authors H.Li, S.Xue, R.Wang
compound source
Molecule: Nop5nop56 Related Protein
Chain: A, C
Fragment: Sequence Database Residues 1-369
Engineered: Yes
Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 186497
Strain: Atcc 43587 Dsm 3638 Jcm 8422 Vc1
Gene: Pf0060
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 50s Ribosomal Protein L7ae
Chain: B, D
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 186497
Strain: Atcc 43587 Dsm 3638 Jcm 8422 Vc1
Gene: Pf1367, Rpl7ae
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'- R(Cpupcpupgpapcpcpgpapapapgpgpcpgpupgpap Gpc)-3');
Chain: E, F
Engineered: Yes
Other_details: Box Cd Rna

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.216 91.841 155.603 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.71 Å
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B
  • ribonuclease P activity


  • Primary referenceStructural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle., Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H, Mol Cell. 2010 Sep 24;39(6):939-49. PMID:20864039
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk]
  • Biological Unit Coordinates (3nvi.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (3nvi.pdb2.gz) 71 Kb
  • Biological Unit Coordinates (3nvi.pdb3.gz) 71 Kb
  • CSU: Contacts of Structural Units for 3NVI
  • Structure Factors (370 Kb)
  • Retrieve 3NVI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NVI from S2C, [Save to disk]
  • Re-refined 3nvi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NVI 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 3NVI
  • 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 3NVI, from MSDmotif at EBI
  • Fold representative 3nvi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nvi] [3nvi_C] [3nvi_F] [3nvi_B] [3nvi_E] [3nvi_A] [3nvi_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NVI: [NOSIC ] by SMART
  • Other resources with information on 3NVI
  • Community annotation for 3NVI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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