1LOJ Rna Binding Protein, Transcription date May 06, 2002
title Crystal Structure Of A Methanobacterial Sm-Like Archaeal Pro (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
authors C.Mura, A.Kozhukhovsky, D.Eisenberg
compound source
Molecule: Small Nuclear Ribonucleoprotein Homolog (Sm-Like)
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N
Synonym: Sm-Like Archaeal Protein Smap1; Putative Snrnp Sm- Protein;
Engineered: Yes
Other_details: Full-Length Smap1 With Additional 5-6 Residu Appended To The C-Terminus (Artefact Of Cloning Vector)
Organism_scientific: Methanothermobacter Thermautotrophicus Delta H;
Organism_taxid: 187420
Strain: Delta H
Gene: Mth649
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b(+)
symmetry Space Group: P 1 21 1
R_factor 0.207 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.254 109.956 83.756 90.00 95.81 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand MPD, U, URI enzyme
related structures by homologous chain: 1I81, 1JBM
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, N, K, E, B, H, M, C, D, I, G, L


Primary referenceThe oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs)., Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D, Protein Sci 2003 Apr;12(4):832-47. PMID:12649441
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (189 Kb) [Save to disk]
  • Biological Unit Coordinates (1loj.pdb1.gz) 93 Kb
  • Biological Unit Coordinates (1loj.pdb2.gz) 91 Kb
  • Biological Unit Coordinates (1loj.pdb3.gz) 180 Kb
  • LPC: Ligand-Protein Contacts for 1LOJ
  • CSU: Contacts of Structural Units for 1LOJ
  • Likely Quarternary Molecular Structure file(s) for 1LOJ
  • Structure Factors (1213 Kb)
  • Retrieve 1LOJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LOJ from S2C, [Save to disk]
  • Re-refined 1loj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LOJ 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 1LOJ
  • 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 1LOJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1loja_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1lojb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1lojc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1lojd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1loje_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1lojf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1lojg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1lojh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1loji_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1lojj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1lojk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1lojl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1lojm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1lojn_, region N [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: [1loj_J] [1loj_A] [1loj_I] [1loj] [1loj_B] [1loj_G] [1loj_F] [1loj_N] [1loj_K] [1loj_E] [1loj_H] [1loj_D] [1loj_C] [1loj_L] [1loj_M]
  • SWISS-PROT database: [O26745]
  • Domain organization of [RUXX_METTH] by SWISSPFAM
  • Domain found in 1LOJ: [Sm ] by SMART
  • Other resources with information on 1LOJ
  • Community annotation for 1LOJ 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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