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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE SALMONELLA TYPE III SECRETION SYSTEM TIP PROTEIN SIPD IN COMPLEX WITH CHENODEOXYCHOLATE
 
Authors :  S. Chatterjee, D. Zhong, B. A. Nordhues, K. P. Battaile, S. Lovell, R. N.
Date :  18 Jul 10  (Deposition) - 17 Nov 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Coiled-Coil, Bacterial Needle Tip Protein, Sipb, Sipc, Prgi, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chatterjee, D. Zhong, B. A. Nordhues, K. P. Battaile, S. Lovell, R. N. De Guzman
The Crystal Structures Of The Salmonella Type Iii Secretion System Tip Protein Sipd In Complex With Deoxycholate And Chenodeoxycholate.
Protein Sci. V. 20 75 2011
PubMed-ID: 21031487  |  Reference-DOI: 10.1002/PRO.537

(-) Compounds

Molecule 1 - CELL INVASION PROTEIN SIPD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDZ1
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SIPD, SSPD, STM2883
    Organism Scientific: SALMONELLA ENTERICA
    Organism Taxid: 90371
    Strain: ENTERICA SEROVAR TYPHIMURIUM
    Synonym: SALMONELLA INVASION PROTEIN D

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1JN31Ligand/IonCHENODEOXYCHOLIC ACID
2NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1JN3-1Ligand/IonCHENODEOXYCHOLIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1JN31Ligand/IonCHENODEOXYCHOLIC ACID
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:36 , HIS A:37 , MET A:38 , HIS A:40BINDING SITE FOR RESIDUE NI A 1
2AC2SOFTWARESER A:221 , GLY A:222 , LYS A:338 , PHE A:340 , ASN B:104 , ALA B:108 , LEU B:318 , ASN B:321 , VAL B:325 , HOH B:436BINDING SITE FOR RESIDUE JN3 B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O02)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:215 -Pro A:216
2Phe B:215 -Pro B:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O02)

(-) Exons   (0, 0)

(no "Exon" information available for 3O02)

(-) 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:283
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:307
                                    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       
           SIPD_SALTY    36 STTEHRGTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSFLQ 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....eeeehhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o02 A  36 GHMEHRGTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAF------------------------IWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSFLQ 342
                                    45        55        65        75        85        95       105   |     -         -       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       
                                                                                                   109                      134                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:290
                                    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
           SIPD_SALTY    47 SLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) IpaD-3o02B01 B:47-336                                                                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) IpaD-3o02B02 B:47-336                                                                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh---...hhhhhhhhhhhh........-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....eeeehhhhhhhhhhhhhhhhh......eee...---.....hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o02 B  47 SLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALA---VSLSAEQNENLRSAFSAPTSALF-----------------WDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQ---GVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
                                    56        66        76        86    |   96       106       116|        -       136       146       156       166       176       186       196       206       216 |   | 226       236       246       256       266       276       286       296       306       316       326       336
                                                                       91  95                   117               135                                                                                218 222
   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  (0, 0)

(no "SCOP Domain" information available for 3O02)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O02)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: IpaD] (6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SIPD_SALTY | Q56026)
biological process
    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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  3o02
    Family and Domain Information: ProDom | SYSTERS
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  SIPD_SALTY | Q56026
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 Related Entries

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

UniProtKB/Swiss-Prot
        SIPD_SALTY | Q56026: 2ym0 2ym9 3nzz 3o00 3o01 3zqb 3zqe

(-) Related Entries Specified in the PDB File

3nzz SAME PROTEIN WITHOUT LIGAND
3o00 SAME PROTEIN WITHOUT LIGAND AND WITH C244S MUTATION
3o01 SAME PROTEIN IN COMPLEX WITH DEOXYCHOLATE