1IPA Transferase date May 02, 2001
title Crystal Structure Of Rna 2'-O Ribose Methyltransferase
authors O.Nureki, M.Shirouzu, K.Hashimoto, R.Ishitani, T.Terada, M.Tamako T.Oshima, M.Chijimatsu, K.Takio, D.G.Vassylyev, T.Shibata, Y.Ino S.Kuramitsu, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Rna 2'-O-Ribose Methyltransferase
Chain: A
Synonym: Rrmh
Ec: 2.1.1.-
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b
symmetry Space Group: P 43 21 2
R_factor 0.226 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.729 66.729 125.684 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand
enzyme Transferase E.C.2.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA methyltransferase activi...


  • Primary referenceAn enzyme with a deep trefoil knot for the active-site architecture., Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S, Acta Crystallogr D Biol Crystallogr 2002 Jul;58(Pt 7):1129-37. PMID:12077432
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (1ipa.pdb1.gz) 43 Kb
  • CSU: Contacts of Structural Units for 1IPA
  • Likely Quarternary Molecular Structure file(s) for 1IPA
  • Structure Factors (104 Kb)
  • Retrieve 1IPA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IPA from S2C, [Save to disk]
  • Re-refined 1ipa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IPA 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 1IPA
  • 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
  • 3D motif for 1IPA, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ipaa2, region A:1-105 [Jmol] [rasmolscript] [script source]
        - Domain d1ipaa1, region A:106-263 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ipa_A] [1ipa]
  • SWISS-PROT database: [Q7SID4]
  • Domain organization of [Q7SID4_THETH] by SWISSPFAM
  • Domain found in 1IPA: [SpoU_sub_bind ] by SMART
  • Other resources with information on 1IPA
  • Community annotation for 1IPA 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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