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(-) Description

Title :  CRYSTAL STRUCTURE OF TREPONEMA PALLIDUM TP0751 (PALLILYSIN)
 
Authors :  M. L. Parker, M. J. Boulanger
Date :  25 Apr 16  (Deposition) - 12 Oct 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Biol. Unit 9:  I  (1x)
Biol. Unit 10:  A,B,C  (2x)
Biol. Unit 11:  D (1x),E (1x),F (1x),G (1x),H (1x),I (1x)
Keywords :  Lipocalin, Outer Membrane Protein, Adhesin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Parker, S. Houston, H. Petrosova, K. V. Lithgow, R. Hof, C. Wetherell, W. C. Kao, Y. P. Lin, T. J. Moriarty, R. Ebady, C. E. Cameron, M. J. Boulanger
The Structure Of Treponema Pallidum Tp0751 (Pallilysin) Reveals A Non-Canonical Lipocalin Fold That Mediates Adhesion To Extracellular Matrix Components And Interaction With Host Cells.
Plos Pathog. V. 12 05919 2016
PubMed-ID: 27683203  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005919

(-) Compounds

Molecule 1 - TP0751
    Chains: A, B, C, D, E, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TP_0751
    Mutation: YES
    Organism Scientific: TREPONEMA PALLIDUM (STRAIN NICHOLS)
    Organism Taxid: 243276
    Strain: NICHOLS

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): A        
Biological Unit 2 (1x):  B       
Biological Unit 3 (1x):   C      
Biological Unit 4 (1x):    D     
Biological Unit 5 (1x):     E    
Biological Unit 6 (1x):      F   
Biological Unit 7 (1x):       G  
Biological Unit 8 (1x):        H 
Biological Unit 9 (1x):         I
Biological Unit 10 (2x): ABC      
Biological Unit 11 (1x):    D (1x)E (1x)F (1x)G (1x)H (1x)I (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5JK2)

(-) Sites  (0, 0)

(no "Site" information available for 5JK2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JK2)

(-) Exons   (0, 0)

(no "Exon" information available for 5JK2)

(-) Sequences/Alignments

Asymmetric 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:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhh.eeeee......eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee......eeeeeeeeee..eeee.eeee.............eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 A  96 QPPVQTAMRIALWNRATHGEQGALQHLLAGLWIQTEDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARLKIGSTSMWDGQYTRYHA 229
                                   105       115       125     ||141       151       161       171       181       191       201       211       221        
                                                             131|                                                                                           
                                                              138                                                                                           


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhhheeeee.....eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee.....eeeeeeeeeee..eeeeeeeeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 B  96 QPPVQTAMRIALWNRATHGEQGALQHLLAGLWIQTDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARLKTSMWDGQYTRYHAG 230
                                   105       115       125    || 142       152       162       172       182       192       202       212||     225     
                                                            130|                                                                        213|             
                                                             138                                                                         217             


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhh.eeeee......eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee.....eeeeeeeeeee..eeeeeeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 C  96 QPPVQTAMRIALWNRATHGEQGALQHLLAGLWIQTGDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARTSMWDGQYTRYH 228
                                   105       115       125    || 141       151       161       171       181       191       201       211|      226  
                                                            130|                                                                       211|           
                                                             137                                                                        217           


Chain D from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhhh.eeee.....eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee.....eeeeeeeeeee..eeeeeeeeee..eee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 D  96 QPPVQTAMRIALWNRATHGEQGALQHLLAGLWIQTDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARLKIGSTSMWDGQYTRYHAG 230
                                   105       115       125    || 142       152       162       172       182       192       202       212       222        
                                                            130|                                                                                            
                                                             138                                                                                            


Chain E from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhheeeee......eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee.....eeeeeeeeeee..eeeeeeeeee............eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 E  97 PPVQTAMRIALWNRATHGEQGALQHLLAGLWIQTGDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARLKIGSTSMWDGQYTRYHAG 230
                                   106       116       126   ||  142       152       162       172       182       192       202       212       222        
                                                           130|                                                                                             
                                                            137                                                                                             


Chain F from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhheeeee.....eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee.....eeeeeeeeeee..eeeeeeeeee............eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 F  97 PPVQTAMRIALWNRATHQGALQHLLAGLWIQTDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARLKIGSTSMWDGQYTRYH 228
                                   106      |118       128 ||    145       155       165       175       185       195       205       215       225   
                                          113|           130|                                                                                          
                                           116            138                                                                                          


Chain G from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhh.eeeee......eeee.....eeeeee..eeeeeeeeeeeee..eeeeeeee......eeeeeeee....eeeeeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 G  98 PVQTAMRIALWNRATHGALQHLLAGLWIQTGDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVATSMWDGQYTRYHA 229
                                   107      |120       130|      146       156       166       176       186       196       206   ||  222       
                                          114|         130|                                                                      210|            
                                           118          137                                                                       217            


Chain H from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....hhhhh.eeeee.....eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee......eeeeeeeeee..eeeeeeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 H  98 PVQTAMRIALWNRATHGEQGALQHLLAGLWIQTDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVASTSMWDGQYTRYH 228
                                   107       117       127  ||   144       154       164       174       184       194       204     ||219         
                                                          130|                                                                     210|            
                                                           138                                                                      216            


Chain I from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...hhhhheeeee.....eeeee....eeeeee..eeeeeeeeeeeee..eeeeeeee.....eeeeeeeeeee..eeeeeeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk2 I  97 PPVQTAMRIALWNRATLQHLLAGLWIQTDIHPLLFFDREHAEITFSRASVQEIFLVDSAHTHRKTVSFLTRNTAISSIRRRLEVTFESHAVIHVRAVEDVARTSMWDGQYTRYHAG 230
                                   106     ||122       139       149       159       169       179       189       199       209 ||    224      
                                         112|        130|                                                                      211|             
                                          119         138                                                                       217
   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  (0, 0)

(no "SCOP Domain" information available for 5JK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JK2)

(-) Gene Ontology  (0, 0)

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5jir