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(-) Description

Title :  TP47, THE 47-KILODALTON LIPOPROTEIN OF TREPONEMA PALLIDUM
 
Authors :  R. K. Deka, M. Machius, M. V. Norgard, D. R. Tomchick
Date :  23 Oct 02  (Deposition) - 01 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipoproteinullntigen, Penicillin-Binding Protein, Integral Membrane Lipoprotein, Immunogen, Four-Domain Protein, Antigen, Lipoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Deka, M. Machius, M. V. Norgard, D. R. Tomchick
Crystal Structure Of The 47-Kda Lipoprotein Of Treponema Pallidum Reveals A Novel Penicillin-Binding Protein
J. Biol. Chem. V. 277 41857 2002
PubMed-ID: 12196546  |  Reference-DOI: 10.1074/JBC.M207402200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 47 KDA MEMBRANE ANTIGEN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA7
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: TREPONEMA PALLIDUM
    Organism Taxid: 160

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1PDX2Ligand/Ion2,3-DI-O-SULFO-ALPHA-D-GLUCOPYRANOSE
2XE5Ligand/IonXENON

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:260 , CYS A:296 , PHE A:331BINDING SITE FOR RESIDUE XE A1415
2AC2SOFTWARELYS A:287 , GLY A:289 , ARG A:290 , VAL A:291 , HOH A:2309 , HOH A:2311 , MET B:234 , VAL B:291 , ARG B:293 , PDX B:1414BINDING SITE FOR RESIDUE PDX A1417
3AC3SOFTWAREVAL A:291 , PDX A:1417 , ARG B:88 , LYS B:287 , GLY B:289 , ARG B:290 , VAL B:291 , ARG B:293 , HOH B:2255 , HOH B:2308BINDING SITE FOR RESIDUE PDX B1414
4AC4SOFTWARETYR B:260 , CYS B:296 , PHE B:331BINDING SITE FOR RESIDUE XE B1415
5AC5SOFTWAREGLU B:72 , MET B:104BINDING SITE FOR RESIDUE XE B1416
6AC6SOFTWAREVAL B:78 , LEU B:79 , TRP B:93BINDING SITE FOR RESIDUE XE B1417

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O75)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O75)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O75)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O75)

(-) Exons   (0, 0)

(no "Exon" information available for 1O75)

(-) 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:399
 aligned with TA47_TREPA | P29723 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:408
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425        
           TA47_TREPA    26 ETHYGYATLSYADYWAGELGQSRDVLLAGNAEADRAGDLDAGMFDAVSRATHGHGAFRQQFQYAVEVLGEKVLSKQETEDSRGRKKWEYETDPSVTKMVRASASFQDLGEDGEIKFEAVEGAVALADRASSFMVDSEEYKITNVKVHGMKFVPVAVPHELKGIAKEKFHFVEDSRVTENTNGLKTMLTEDSFSARKVSSMESPHDLVVDTVGTGYHSRFGSDAEASVMLKRADGSELSHREFIDYVMNFNTVRYDYYGDDASYTNLMASYGTKHSADSWWKTGRVPRISCGINYGFDRFKGSGPGYYRLTLIANGYRDVVADVRFLPKYEGNIDIGLKGKVLTIGGADAETLMDAAVDVFADGQPKLVSDQAVSLGQNVLSADFTPGTEYTVEVRFKEFGSVRAKVVA 433
               SCOP domains d1o75a3 A:7-206 Tp47 lipopro         tein, N-terminal domain                                                                                                                                            d1o75a1 A:207-332 Tp47 lipoprotein, middle and C-terminal domains                                                             d1o75a2 A:333-414 Tp47 lipoprotein, middle and C-terminal domains                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1o75A03 A:205-332  [code=2.60.40.1300, no name defined]                                                                         1o75A04 A:333-414  [code=2.60.40.1270, no name defined]                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhh..hhhhh.---------.........eeee..hhhhhhhh..eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee.eeeeee.....eeeee..................eeeeeeeeeeeeeeeeeeeee..hhhhhhhhhh.ee.................................eeeeeee..........eeeeeeeee......hhhhhhhhhh.eeeeeeee...........eee.......ee.......eeeeee...hhhhh....eeeeeeeee.....eeeeeee........eeeeeeeeeeee.........eeeeeee......eeeeee..eeeeeeeee....eeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o75 A   7 ETSYGYATLSYADYWAGELGQSRDVLLA---------DLDAGMFDAVSRATHGHGAFRQQFQYAVEVLGEKVLSKQETEDSRGRKKWEYETDPSVTKMVRASASFQDLGEDGEIKFEAVEGAVALADRASSFMVDSEEYKITNVKVHGMKFVPVAVPHELKGIAKEKFHFVEDSRVTENTNGLKTMLTEDSFSARKVSSMESPHDLVVDTVGTGYHSRFGSDAEASVMLKRADGSELSHREFIDYVMNFNTVRYDYYGDDASYTNLMASYGTKHSADSWWKTGRVPRISCGINYGFDRFKGSGPGYYRLTLIANGYRDVVADVRFLPKYEGNIDIGLKGKVLTIGGADAETLMDAAVDVFADGQPKLVSDQAVSLGQNVLSADFTPGTEYTVEVRFKEFGSVRAKVVA 414
                                    16        26       | -       |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       326       336       346       356       366       376       386       396       406        
                                                      34        44                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:402
 aligned with TA47_TREPA | P29723 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:407
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       
           TA47_TREPA    26 ETHYGYATLSYADYWAGELGQSRDVLLAGNAEADRAGDLDAGMFDAVSRATHGHGAFRQQFQYAVEVLGEKVLSKQETEDSRGRKKWEYETDPSVTKMVRASASFQDLGEDGEIKFEAVEGAVALADRASSFMVDSEEYKITNVKVHGMKFVPVAVPHELKGIAKEKFHFVEDSRVTENTNGLKTMLTEDSFSARKVSSMESPHDLVVDTVGTGYHSRFGSDAEASVMLKRADGSELSHREFIDYVMNFNTVRYDYYGDDASYTNLMASYGTKHSADSWWKTGRVPRISCGINYGFDRFKGSGPGYYRLTLIANGYRDVVADVRFLPKYEGNIDIGLKGKVLTIGGADAETLMDAAVDVFADGQPKLVSDQAVSLGQNVLSADFTPGTEYTVEVRFKEFGSVRAKVV 432
               SCOP domains d1o75b3 B:7-206 Tp47 lipopro     tein, N-terminal domain                                                                                                                                                d1o75b1 B:207-332 Tp47 lipoprotein, middle and C-terminal domains                                                             d1o75b2 B:333-413 Tp47 lipoprotein, middle and C-terminal domains                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1o75B03 B:205-332  [code=2.60.40.1300, no name defined]                                                                         1o75B04 B:333-413  [code=2.60.40.1270, no name defined]                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhh..hhhhh.-----.............eeee..hhhhhhhh..eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee.eeeeee.....eeeee..................eeeeeeeeeeeeeeeeeeeee..hhhhhhhhh..ee.................................eeeeeeeee........eeeeeeeee......hhhhhhhhhh.eeeeeeee...........eee.......ee.......eeeeee...hhhhh....eeeeeeeee.....eeeeeee........eeeee..eeeee..........eeeeee....eeeeeee...eeee..........eeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o75 B   7 ETSYGYATLSYADYWAGELGQSRDVLLA-----DRAGDLDAGMFDAVSRATHGHGAFRQQFQYAVEVLGEKVLSKQETEDSRGRKKWEYETDPSVTKMVRASASFQDLGEDGEIKFEAVEGAVALADRASSFMVDSEEYKITNVKVHGMKFVPVAVPHELKGIAKEKFHFVEDSRVTENTNGLKTMLTEDSFSARKVSSMESPHDLVVDTVGTGYHSRFGSDAEASVMLKRADGSELSHREFIDYVMNFNTVRYDYYGDDASYTNLMASYGTKHSADSWWKTGRVPRISCGINYGFDRFKGSGPGYYRLTLIANGYRDVVADVRFLPKYEGNIDIGLKGKVLTIGGADAETLMDAAVDVFADGQPKLVSDQAVSLGQNVLSADFTPGTEYTVEVRFKEFGSVRAKVV 413
                                    16        26       | -   |    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       326       336       346       356       366       376       386       396       406       
                                                      34    40
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O75)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TA47_TREPA | P29723)
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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  1o75
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