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(-) Description

Title :  CLOSTRIDIUM PERFRINGENS DELTA-TOXIN
 
Authors :  J. Huyet, C. E. Naylor, M. Gibert, M. R. Popoff, A. K. Basak
Date :  20 Apr 11  (Deposition) - 16 May 12  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Toxin, Beta-Pore-Forming Toxin, Haemolysin, Enterotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Huyet, C. E. Naylor, C. G. Savva, M. Gibert, M. R. Popoff, A. K. Basak
Structural Insights Into Clostridium Perfringens Delta Toxi Pore Formation.
Plos One V. 8 66673 2013
PubMed-ID: 23805259  |  Reference-DOI: 10.1371/JOURNAL.PONE.0066673
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DELTA TOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS RIL
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 29-318
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Strain: CP24-03

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2IMD1Ligand/IonIMIDAZOLE
3ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:52 , TRP A:281 , HIS A:284 , HOH A:2220BINDING SITE FOR RESIDUE ZN A1291
2AC2SOFTWAREASP A:164 , GLU A:177 , HOH A:2080 , HOH A:2082 , HOH A:2134 , HOH A:2141BINDING SITE FOR RESIDUE ZN A1292
3AC3SOFTWAREASP A:34 , ARG A:287 , GLN A:288 , ZN A:1297 , HOH A:2219BINDING SITE FOR RESIDUE IMD A1293
4AC4SOFTWARELYS A:54 , GLY A:203 , TRP A:257 , TRP A:261 , HOH A:2221BINDING SITE FOR RESIDUE GOL A1294
5AC5SOFTWARESER A:199 , ARG A:200 , TYR A:201 , SER A:202 , HOH A:2159 , HOH A:2222BINDING SITE FOR RESIDUE GOL A1295
6AC6SOFTWAREILE A:106 , ASP A:164 , THR A:165 , ASN A:166 , GLU A:177 , ASN A:183 , HOH A:2126 , HOH A:2128 , HOH A:2141 , HOH A:2223BINDING SITE FOR RESIDUE GOL A1296
7AC7SOFTWAREASP A:34 , IMD A:1293 , HOH A:2219 , HOH A:3001BINDING SITE FOR RESIDUE ZN A1297

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YGT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:110 -Pro A:111
2Ser A:139 -Leu A:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YGT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YGT)

(-) Exons   (0, 0)

(no "Exon" information available for 2YGT)

(-) 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:283
 aligned with B8QGZ7_CLOPF | B8QGZ7 from UniProtKB/TrEMBL  Length:318

    Alignment length:283
                                                                                                                                                                                                                                                                                                                   318 
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316 | 
         B8QGZ7_CLOPF    37 IRKEENGNVTIITQNNKQIRKYSSTDSATTKSNSKITVDASFVDDKFSSEMTTIISLKGFIPSGRKIFALSKYRGVMRWPIKYMVDLKNNSLDSSVKIVDSVPKNTISTKEVNNTISYSIGGGIDTSNKASLNANYAVSKSISYVQPDYNTIQTNDTNSIASWNTEFAETRDGYNVNSWNIVYGNQMFMRSRYSGTSTTNFTPDYQLSSLITGGFSPNFGVVLTAPNGTKKSQIEISLKREINSYHIAWDTEWQGRNYPDSKIEETVKFELDWEKHTIRQIS-   -
               SCOP domains d2ygta_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeee..eeeeeeeeeeeee.....eeeeeeeeee......eeeeeeeeeeee...eeee....eeeeeeeeeeeeeeee.hhhhh.eeeeee...ee...eeeeeeee.....eeee..........eeeeeeee...eeeeeeee...eeeeeeee...................................hhhhhhhhhhhee..eeeeeeee.....eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ygt A   9 IRKEENGNVTIITQNNKQIRKYSSTDSATTKSNSKITVDASFVDDKFSSEMTTIISLKGFIPSGRKIFALSKYRGVMRWPIKYMVDLKNNSLDSSVKIVDSVPKNTISTKEVNNTISYSIGGGIDTSNKASLNANYAVSKSISYVQPDYNTIQTNDTNSIASWNTEFAETRDGYNVNSWNIVYGNQMFMRSRYSGTSTTNFTPDYQLSSLITGGFSPNFGVVLTAPNGTKKSQIEISLKREINSYHIAWDTEWQGRNYPDSKIEETVKFELDWEKHTIRQISH 291
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YGT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YGT)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B8QGZ7_CLOPF | B8QGZ7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0051715    cytolysis in other organism    The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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    Ser A:139 - Leu A:140   [ RasMol ]  
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