3NVM Transferase date Jul 08, 2010
title Structural Basis For Substrate Placement By An Archaeal Box Ribonucleoprotein Particle
authors S.Xue, R.Wang, H.Li
compound source
Molecule: Nop5nop56 Related Protein
Chain: A
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: Fibrillarin-Like Rrnatrna 2'-O-Methyltransferase
Chain: B
Ec: 2.1.1.-
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 186497
Strain: Atcc 43587 Dsm 3638 Jcm 8422 Vc1
Gene: Flpa, Pf0059
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 1 2
R_factor 0.242 R_Free 0.316
length a length b length c angle alpha angle beta angle gamma
100.623 100.623 265.355 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.41 Å
enzyme Transferase E.C.2.1.1 BRENDA


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] (208 Kb) [Save to disk]
  • Biological Unit Coordinates (3nvm.pdb1.gz) 203 Kb
  • CSU: Contacts of Structural Units for 3NVM
  • Structure Factors (273 Kb)
  • Retrieve 3NVM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NVM from S2C, [Save to disk]
  • Re-refined 3nvm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NVM 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 3NVM
  • 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 3NVM, from MSDmotif at EBI
  • Fold representative 3nvm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nvm_B] [3nvm] [3nvm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NVM: [Fibrillarin] [NOSIC ] by SMART
  • Other resources with information on 3NVM
  • Community annotation for 3NVM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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