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(-) Description

Title :  BIPD OF BURKHOLDERIA PSEUDOMALLEI
 
Authors :  S. Johnson, P. Roversi, T. Field, J. E. Deane, E. E. Galyov, S. M. Lea
Date :  16 Nov 06  (Deposition) - 20 Nov 06  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Burkholderia Pseudomallei, Bipd, Ttss, T3Ss, Type 3 Secretion System, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Johnson, P. Roversi, M. Espina, A. Olive, J. E. Deane, S. Birket, T. Field, W. D. Picking, A. J. Blocker, E. E. Galyov, W. L. Picking, S. M. Lea
Self-Chaperoning Of The Type Iii Secretion System Needle Tip Proteins Ipad And Bipd.
J. Biol. Chem. V. 282 4035 2007
PubMed-ID: 17077085  |  Reference-DOI: 10.1074/JBC.M607945200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEMBRANE ANTIGEN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEXBIPD
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PGEX-4T-1
    Fragment: RESIDUES 10-310
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Other Details: PUBLIC HEALTH LABORATORY SERVICE, COLINDALE, LONDON, UK
    Strain: 10276
    Synonym: BIPD

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1BO32Ligand/IonBORIC ACID
2FLC1Ligand/IonCITRATE ANION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BO31Ligand/IonBORIC ACID
2FLC1Ligand/IonCITRATE ANION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BO31Ligand/IonBORIC ACID
2FLC-1Ligand/IonCITRATE ANION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:65 , GLY A:77 , ARG A:78BINDING SITE FOR RESIDUE FLC A1303
2AC2SOFTWARELYS A:167 , LEU A:168 , TYR A:171 , LYS A:186 , ILE A:187 , LEU A:190 , HOH A:2014BINDING SITE FOR RESIDUE BO3 A1302
3AC3SOFTWARELYS B:167 , LEU B:168 , TYR B:171 , LYS B:186 , ILE B:187 , LEU B:190BINDING SITE FOR RESIDUE BO3 B1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J9T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J9T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J9T)

(-) Exons   (0, 0)

(no "Exon" information available for 2J9T)

(-) 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:252
 aligned with BIPD_BURPS | Q63K37 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:267
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
           BIPD_BURPS    35 MTDDDLRAAGVDRRVPEQKLGAAIDEFASLRLPDRIDGRFVDGRRANLTVFDDARVAVRGHARAQRNLLERLETELLGGTLDTAGDEGGIQPDPILQGLVDVIGQGKSDIDAYATIVEGLTKYFQSVADVMSKLQDYISAKDDKNMKIDGGKIKALIQQVIDHLPTMQLPKGADIARWRKELGDAVSISDSGVVTINPDKLIKMRDSLPPDGTVWDTARYQAWNTAFSGQKDNIQNDVQTLVEKYSHQNSNFDNLVKVLSGAISTLT 301
               SCOP domains d2j9ta1 A:35-301 Putative membrane antigen BipD                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhhhhhhhhhhh...eee..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeehhhhhhhhhhhhhhh..eee.....hhhhhhhhhh..eee....eeee.hhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9t A  35 MTDDDLRAAGVDRRVPEQKLGAAIDEFASLRLPDRIDGRFVDGRRANLTVFDDARVAVRGHARAQRNLLERLETELL---------------DPILQGLVDVIGQGKSDIDAYATIVEGLTKYFQSVADVMSKLQDYISAKDDKNMKIDGGKIKALIQQVIDHLPTMQLPKGADIARWRKELGDAVSISDSGVVTINPDKLIKMRDSLPPDGTVWDTARYQAWNTAFSGQKDNIQNDVQTLVEKYSHQNSNFDNLVKVLSGAISTLT 301
                                    44        54        64        74        84        94       104      |  -         -  |    134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
                                                                                                      111             127                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with BIPD_BURPS | Q63K37 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:267
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
           BIPD_BURPS    35 MTDDDLRAAGVDRRVPEQKLGAAIDEFASLRLPDRIDGRFVDGRRANLTVFDDARVAVRGHARAQRNLLERLETELLGGTLDTAGDEGGIQPDPILQGLVDVIGQGKSDIDAYATIVEGLTKYFQSVADVMSKLQDYISAKDDKNMKIDGGKIKALIQQVIDHLPTMQLPKGADIARWRKELGDAVSISDSGVVTINPDKLIKMRDSLPPDGTVWDTARYQAWNTAFSGQKDNIQNDVQTLVEKYSHQNSNFDNLVKVLSGAISTLT 301
               SCOP domains d2j9tb_ B: Putative membrane antigen BipD                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhhhhhhhhhhh...eee..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeehhhhhhhhhhhhhhh..eee.....hhhhhhhhhh..eee....eeee.hhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9t B  35 MTDDDLRAAGVDRRVPEQKLGAAIDEFASLRLPDRIDGRFVDGRRANLTVFDDARVAVRGHARAQRNLLERLETELL---------------DPILQGLVDVIGQGKSDIDAYATIVEGLTKYFQSVADVMSKLQDYISAKDDKNMKIDGGKIKALIQQVIDHLPTMQLPKGADIARWRKELGDAVSISDSGVVTINPDKLIKMRDSLPPDGTVWDTARYQAWNTAFSGQKDNIQNDVQTLVEKYSHQNSNFDNLVKVLSGAISTLT 301
                                    44        54        64        74        84        94       104      |  -         -  |    134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
                                                                                                      111             127
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J9T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J9T)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BIPD_BURPS | Q63K37)
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
        BIPD_BURPS | Q63K37: 2ixr 2izp 3nft

(-) Related Entries Specified in the PDB File

2ixr BIPD OF BURKHOLDERIA PSEUDOMALLEI
2izp BIPD - AN INVASION PRTEIN ASSOCIATED WITH THE TYPE-III SECRETION SYSTEM OF BURKHOLDERIA PSEUDOMALLEI.