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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIC C-TERMINAL DOMAIN OF TONB
 
Authors :  C. Chang, A. Mooser, A. Pluckthun, A. Wlodawer
Date :  20 Apr 01  (Deposition) - 01 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Novel Fold, Intertwined Dimer, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Chang, A. Mooser, A. Pluckthun, A. Wlodawer
Crystal Structure Of The Dimeric C-Terminal Domain Of Tonb Reveals A Novel Fold.
J. Biol. Chem. V. 276 27535 2001
PubMed-ID: 11328822  |  Reference-DOI: 10.1074/JBC.M102778200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TONB PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPAT37
    Expression System StrainXLI-BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN RESIDUES 164-239
    GeneJM83
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1BR4Ligand/IonBROMIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:166 , GLU A:216 , HOH A:365BINDING SITE FOR RESIDUE BR A 301
2AC2SOFTWAREARG A:212 , HOH A:334BINDING SITE FOR RESIDUE BR A 302
3AC3SOFTWAREGLY A:174 , GLN A:175 , HOH B:356BINDING SITE FOR RESIDUE BR B 303
4AC4SOFTWAREARG B:166 , TYR B:215 , GLU B:216BINDING SITE FOR RESIDUE BR B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IHR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IHR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TONB_ECOLI_006 *V176ITONB_ECOLI  ---  ---A/BV176I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IHR)

(-) Exons   (0, 0)

(no "Exon" information available for 1IHR)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:73
 aligned with TONB_ECOLI | P02929 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:73
                                   174       184       194       204       214       224       234   
           TONB_ECOLI   165 ARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTE 237
               SCOP domains d1ihra_ A: TonB                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhh.......eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------I------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 1ihr A 165 ARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTE 237
                                   174       184       194       204       214       224       234   

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with TONB_ECOLI | P02929 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:74
                                   174       184       194       204       214       224       234    
           TONB_ECOLI   165 ARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEI 238
               SCOP domains d1ihrb_ B: TonB                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeee.....eeeeeee.....hhhhhhhhhhhh.........eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------I-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1ihr B 165 ARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEI 238
                                   174       184       194       204       214       224       234    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1IHR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IHR)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TONB_ECOLI | P02929)
molecular function
    GO:0031992    energy transducer activity    The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015343    siderophore transmembrane transporter activity    Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).
biological process
    GO:0043213    bacteriocin transport    The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
    GO:0015889    cobalamin transport    The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0042914    colicin transport    The directed movement of a colicin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0044718    siderophore transmembrane transport    The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore.
    GO:0015891    siderophore transport    The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0031233    intrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TONB_ECOLI | P029291qxx 1u07 1xx3 2grx 2gsk

(-) Related Entries Specified in the PDB File

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