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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE SALMONELLA TYPE III SECRETION SYSTEM TIP PROTEIN SIPD IN COMPLEX WITH DEOXYCHOLATE
 
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
    Mutation: YES
    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
1DXC1Ligand/Ion(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DXC-1Ligand/Ion(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DXC1Ligand/Ion(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC 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
2AC2SOFTWAREILE A:45 , SER A:221 , GLY A:222 , LYS A:338 , PHE A:340 , HOH A:367 , ASN B:321 , VAL B:325 , HOH B:374BINDING SITE FOR RESIDUE DXC B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O01)

(-) 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 3O01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O01)

(-) Exons   (0, 0)

(no "Exon" information available for 3O01)

(-) 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.....eeeehhhhhhhhhhhhhhhhhh.....eee...........hhhhhhhhhhhh..hhh.eeee..eeeee..hhhhhhhhhhhhh.........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o01 A  36 GHMEHRGTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAF------------------------IWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSSLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSFLQ 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:280
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:297
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           SIPD_SALTY    42 GTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAK 338
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) IpaD-3o01B01 B:42-338                                                                                                                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) IpaD-3o01B02 B:42-338                                                                                                                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........---------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeeehhhhhhhhhhhhhhhhhh.....eee....--.....hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o01 B  42 GTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFS---------------IWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQS--GVKVATEAEARQWLSELNLPNSSLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAK 338
                                    51        61        71        81        91       101       111      |  -         -  |    141       151       161       171       181       191       201       211       | -|      231       241       251       261       271       281       291       301       311       321       331       
                                                                                                      118             134                                                                                  219  |                                                                                                                    
                                                                                                                                                                                                              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 3O01)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O01)

(-) 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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  3o01
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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 3o02 3zqb 3zqe

(-) Related Entries Specified in the PDB File

3nzz THE SAME PROTEIN WITHOUT LIGAND
3o00 THE SAME PROTEIN WITHOUT LIGAND AND WITH C244S MUTATION
3o02