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(-) Description

Title :  TRUNCATED SIPD FROM SALMONELLA TYPHIMURIUM
 
Authors :  M. Lunelli, M. Kolbe
Date :  06 Jun 11  (Deposition) - 17 Aug 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Invasion, Type 3 Secretion, T3Ss, Needle Tip Protein, Host Pathogen Interaction, Bacterial Pathogenesis, Tip Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lunelli, R. Hurwitz, J. Lambers, M. Kolbe
Crystal Structure Of Prgi-Sipd: Insight Into A Secretion Competent State Of The Type Three Secretion System Needle Tip And Its Interaction With Host Ligands
Plos Pathog. V. 7 02163 2011
PubMed-ID: 21829362  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002163

(-) Compounds

Molecule 1 - CELL INVASION PROTEIN SIPD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-28A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 132-343
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 216597
    Strain: SL1344
    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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:263 , GLN A:266 , ASP A:267 , SER B:250BINDING SITE FOR RESIDUE GOL A1329

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YM0)

(-) 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 2YM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YM0)

(-) Exons   (0, 0)

(no "Exon" information available for 2YM0)

(-) 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:199
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:199
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320         
           SIPD_SALTY   131 DAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSST 329
               SCOP domains d2ym0a_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeeehhhhhhhhhhhhhhhh.......eee...........hhhhhhhhhhhh..hhh.eeee..eeeee..hhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ym0 A 131 MAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSST 329
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320         


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:200
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
           SIPD_SALTY   131 DAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTI 330
               SCOP domains d2ym0b_ B: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeeehhhhhhhhhhhhhhhh.......eee...........hhhhhhhhhhhh..hhh.eeee..eeeee..hhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ym0 B 131 MAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTI 330
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YM0)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        SIPD_SALTY | Q56026: 2ym9 3nzz 3o00 3o01 3o02 3zqb 3zqe

(-) Related Entries Specified in the PDB File

2ym9 SIPD FROM SALMONELLA TYPHIMURIUM
3zqb PRGI-SIPD FROM SALMONELLA TYPHIMURIUM
3zqe PRGI-SIPD FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH DEOXYCHOLATE