1K3R Structural Genomics, Unknown Function date Oct 03, 2001
title Crystal Structure Of The Methyltransferase With A Knot From Methanobacterium Thermoautotrophicum
authors T.I.Zarembinski, Y.Kim, K.Peterson, D.Christendat, A.Dharamsi, C.H.Arrowsmith, A.M.Edwards, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg)
compound source
Molecule: Conserved Protein Mt0001
Chain: A, B
Engineered: Yes
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 145262
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.307 51.353 109.250 90.00 94.69 90.00
method X-Ray Diffractionresolution 2.30 Å
Primary referenceDeep trefoil knot implicated in RNA binding found in an archaebacterial protein., Zarembinski TI, Kim Y, Peterson K, Christendat D, Dharamsi A, Arrowsmith CH, Edwards AM, Joachimiak A, Proteins 2003 Feb 1;50(2):177-83. PMID:12486711
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1k3r.pdb1.gz) 86 Kb
  • CSU: Contacts of Structural Units for 1K3R
  • Likely Quarternary Molecular Structure file(s) for 1K3R
  • Structure Factors (174 Kb)
  • Retrieve 1K3R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K3R from S2C, [Save to disk]
  • Re-refined 1k3r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1K3R 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 1K3R
  • 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 1K3R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k3ra2, region A:1-92,A:164-262 [Jmol] [rasmolscript] [script source]
        - Domain d1k3ra1, region A:93-163 [Jmol] [rasmolscript] [script source]
        - Domain d1k3rb2, region B:1-92,B:164-264 [Jmol] [rasmolscript] [script source]
        - Domain d1k3rb1, region B:93-163 [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: [1k3r_A] [1k3r_B] [1k3r]
  • SWISS-PROT database: [O26109]
  • Domain organization of [O26109_METTH] by SWISSPFAM
  • Other resources with information on 1K3R
  • Community annotation for 1K3R 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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