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(-) Description

Title :  STRUCTURE OF TYPHOID TOXIN
 
Authors :  X. Gao, J. Song, J. Galan
Date :  16 Apr 13  (Deposition) - 17 Jul 13  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Complex, Bacterial Toxin, Sugar, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Song, X. Gao, J. E. Galan
Structure And Function Of The Salmonella Typhi Chimaeric A(2)B(5) Typhoid Toxin.
Nature V. 499 350 2013
PubMed-ID: 23842500  |  Reference-DOI: 10.1038/NATURE12377

(-) Compounds

Molecule 1 - PUTATIVE PERTUSSIS-LIKE TOXIN SUBUNIT
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 24-137
    Gene: STY1891, T1107
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI
    Organism Taxid: 90370
 
Molecule 2 - CYTOLETHAL DISTENDING TOXIN SUBUNIT B HOMOLOG
    Chains: F
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-269
    Gene: CDTB, STY1886, T1111
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI
    Organism Taxid: 90370
    Synonym: CDT B, DEOXYRIBONUCLEASE CDTB
 
Molecule 3 - PUTATIVE PERTUSSIS-LIKE TOXIN SUBUNIT
    Chains: G
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 19-242
    Gene: STY1890, T1108
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI
    Organism Taxid: 90370

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:24 , TRP A:25 , ASP A:28 , HOH A:315 , ASP B:48 , TYR B:110BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREGLU B:24 , TRP B:25 , ASP B:28 , ASP D:48 , TYR D:110BINDING SITE FOR RESIDUE GOL B 201
3AC3SOFTWAREARG A:90 , ASP C:87 , ARG C:90 , TYR C:91 , GLU G:237 , LEU G:238BINDING SITE FOR RESIDUE GOL C 201
4AC4SOFTWAREGLU D:24 , TRP D:25 , ASP D:28 , ASP E:48 , TYR E:110BINDING SITE FOR RESIDUE GOL D 201
5AC5SOFTWAREASP E:48 , GLN E:75 , TRP E:108 , TYR E:110 , PHE E:113BINDING SITE FOR RESIDUE GOL E 201
6AC6SOFTWAREASP C:48 , TYR C:110 , GLU E:24 , TRP E:25 , ASP E:28BINDING SITE FOR RESIDUE GOL E 202
7AC7SOFTWARECYS F:269BINDING SITE FOR RESIDUE GOL F 301
8AC8SOFTWAREASP F:60 , GLN F:128 , ARG G:45 , ARG G:64 , PHE G:185BINDING SITE FOR RESIDUE GOL G 301

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:70
2A:128 -A:133
3B:54 -B:70
4B:128 -B:133
5C:54 -C:70
6C:128 -C:133
7D:54 -D:70
8D:128 -D:133
9E:54 -E:70
10E:128 -E:133
11F:269 -G:214
12G:56 -G:207

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly F:228 -Gly F:229
2Pro G:189 -Gln G:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K6L)

(-) Exons   (0, 0)

(no "Exon" information available for 4K6L)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6l A  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6l B  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6l C  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain D from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6l D  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain E from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeee..eeeeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6l E  24 EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK 137
                                    33        43        53        63        73        83        93       103       113       123       133    


Chain F from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains d4k6lf_ F: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee......hhhhhhhhhhhhhhh......eeeee.........ee.......ee.....eeeeee........eeeeeee..........eeeee.....eeeee.........eeeeee..eeeee.........hhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhh.....eeee.............eeeeee....hhh.eeeee..........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k6l F  23 NISDYKVMTWNLQGSSASTESKWNVNVRQLLSGTAGVDILMVQEAGAVPTSAVPTGRHIQPFGVGIPIDEYTWNLGTTSRQDIRYIYHSAIDVGARRVNLAIVSRQRADNVYVLRPTTVASRPVIGIGLGNDVFLTAHALASGGPDAAAIVRVTINFFRQPQMRHLSWFLAGDFNRSPDRLENDLMTEHLERVVAVLAPTEPTQIGGGILDYGVIVDRAPYSQRVEALRNPQLASDHYPVAFLARSC 269
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       


Chain G from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains d4k6lg_ G: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhh........hhhhhhh.............eeee.hhhhhhhhhhhhhh.......eeeeeee....eeehhhhhhhhhhh....hhhhhhhhhh..eeee....hhh.eeeeeeeee......eeeeeeee..............................eee...ee.hhhhhhh................eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k6l G  19 VDFVYRVDSTPPDVIFRDGFSLLGYNRNFQQFISGRSCSGGSSDSRYIATTSSVNQTYAIARAYYSRSTFKGNLYRYQIRADNNFYSLLPSITYLETQGGHFNAYEKTMMRLQREYVSTLSILPENIQKAVALVYDSATGLVKDGVSTMNASYLGLSTTSNPGVIPFLPEPQTYTQQRIDAFGPLISSCFSIGSVCHSHRGQRADVYNMSFYDARPVIELILSK 242
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K6L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K6L)

(-) Gene Ontology  (9, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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