1SMX Hydrolase date Mar 09, 2004
title Crystal Structure Of The S1 Domain Of Rnase E From E. Coli (Native)
authors M.Schubert, R.E.Edge, P.Lario, M.A.Cook, N.C.J.Strynadka, G.A.Mackie, L.P.Mcintosh
compound source
Molecule: Ribonuclease E
Chain: A, B
Fragment: S1 Domain (Residues 35-125)
Synonym: Rnase E
Ec: 3.1.4.-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rne
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 41 21 2
R_factor 0.199 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
70.378 70.378 87.917 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
enzyme Hydrolase E.C.3.1.4 BRENDA
related structures by homologous chain: 1SN8
A, B

Primary referenceStructural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces., Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP, J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:15312761
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (1smx.pdb1.gz) 32 Kb
  • CSU: Contacts of Structural Units for 1SMX
  • Likely Quarternary Molecular Structure file(s) for 1SMX
  • Structure Factors (143 Kb)
  • Retrieve 1SMX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SMX from S2C, [Save to disk]
  • Re-refined 1smx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SMX 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 1SMX
  • 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 1SMX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1smxa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1smxb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1smx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1smx] [1smx_A] [1smx_B]
  • SWISS-PROT database: [P21513]
  • Domain organization of [RNE_ECOLI] by SWISSPFAM
  • Domain found in 1SMX: [S1 ] by SMART
  • Other resources with information on 1SMX
  • Community annotation for 1SMX 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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