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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  L. J. Gourlay, C. Peri, O. Conchillo-Sole, M. Ferrer-Navarro, A. Gori, D. Rinchai, G. Lertmemongkolchai, P. Lassaux, X. Daura, G. Colombo, M. Bolognesi
Date :  03 Aug 12  (Deposition) - 14 Aug 13  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Lipid Transport, Pal-Tol Complex, Acute Burkholderia Pseuodomallei Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Gourlay, C. Peri, M. Ferrer-Navarro, O. Conchillo-Sole, A. Gori D. Rinchai, R. J. Thomas, O. L. Champion, S. L. Michell, C. Kewcharoenwong, A. Nithichanon, P. Lassaux, L. Perletti, R. Longhi, G. Lertmemongkolchai, R. W. Titball, X. Daura, G. Colombo, M. Bolognesi
Exploiting The Burkholderia Pseudomallei Acute Phase Antige Bpsl2765 For Structure-Based Epitope Discovery/Design In Structural Vaccinology.
Chem. Biool. V. 20 1147 2013
PubMed-ID: 23993463  |  Reference-DOI: 10.1016/J.CHEMBIOL.2013.07.010

(-) Compounds

Molecule 1 - PUTATIVE OMPA FAMILY LIPOPROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PET14B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 36-170
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Strain: K96423
    Synonym: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , THR A:104 , ASP A:105 , ARG A:107 , ASN A:113 , LEU A:116 , ARG A:120 , ARG A:162BINDING SITE FOR RESIDUE ACT A 1171
2AC2SOFTWAREPHE B:70 , ASP B:105 , ARG B:107 , ASN B:113 , LEU B:116 , ARG B:120 , ARG B:162BINDING SITE FOR RESIDUE ACT B 1170
3AC3SOFTWAREPHE C:70 , ASP C:71 , THR C:104 , ASP C:105 , ARG C:107 , ASN C:113 , LEU C:116 , ARG C:120 , ARG C:162BINDING SITE FOR RESIDUE ACT C 1170

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B5C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B5C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B5C)

(-) Exons   (0, 0)

(no "Exon" information available for 4B5C)

(-) 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:119
 aligned with Q63RA7_BURPS | Q63RA7 from UniProtKB/TrEMBL  Length:170

    Alignment length:119
                                    61        71        81        91       101       111       121       131       141       151       161         
         Q63RA7_BURPS    52 DPLNDPNSPLAKRSVYFDFDSYSVQDQYQALLQQHAQYLKSHPQRHILIQGNTDERGTSEYNLALGQKRAEAVRRALSLLGVGDAQMEAVSLGKEKPVALGHDEASWAQNRRADLVYQQ 170
               SCOP domains d4b5ca_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..hhhhh.eee........hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5c A  52 DPLNDPNSPLAKRSVYFDFDSYSVQDQYQALLQQHAQYLKSHPQRHILIQGNTDERGTSEYNLALGQKRAEAVRRALSLLGVGDAQMEAVSLGKEKPVALGHDEASWAQNRRADLVYQQ 170
                                    61        71        81        91       101       111       121       131       141       151       161         


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with Q63RA7_BURPS | Q63RA7 from UniProtKB/TrEMBL  Length:170

    Alignment length:120
                                    59        69        79        89        99       109       119       129       139       149       159       169
         Q63RA7_BURPS    50 TVDPLNDPNSPLAKRSVYFDFDSYSVQDQYQALLQQHAQYLKSHPQRHILIQGNTDERGTSEYNLALGQKRAEAVRRALSLLGVGDAQMEAVSLGKEKPVALGHDEASWAQNRRADLVYQ 169
               SCOP domains d4b5cb_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..hhhhh.eee........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4b5c B  50 TVDPLNDPNSPLAKRSVYFDFDSYSVQDQYQALLQQHAQYLKSHPQRHILIQGNTDERGTSEYNLALGQKRAEAVRRALSLLGVGDAQMEAVSLGKEKPVALGHDEASWAQNRRADLVYQ 169
                                    59        69        79        89        99       109       119       129       139       149       159       169


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with Q63RA7_BURPS | Q63RA7 from UniProtKB/TrEMBL  Length:170

    Alignment length:118
                                    61        71        81        91       101       111       121       131       141       151       161        
         Q63RA7_BURPS    52 DPLNDPNSPLAKRSVYFDFDSYSVQDQYQALLQQHAQYLKSHPQRHILIQGNTDERGTSEYNLALGQKRAEAVRRALSLLGVGDAQMEAVSLGKEKPVALGHDEASWAQNRRADLVYQ 169
               SCOP domains d4b5cc_ C: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.eee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5c C  52 DPLNDPNSPLAKRSVYFDFDSYSVQDQYQALLQQHAQYLKSHPQRHILIQGNTDERGTSEYNLALGQKRAEAVRRALSLLGVGDAQMEAVSLGKEKPVALGHDEASWAQNRRADLVYQ 169
                                    61        71        81        91       101       111       121       131       141       151       161
   Legend:   → Mismatch (orange background)
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  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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B5C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B5C)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q63RA7_BURPS | Q63RA7)
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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4b54 THE STRUCTURE OF THE INACTIVE MUTANT G153R OF LPTC FROM E. COLI