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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF SHAFT PILIN SPAA FROM LACTOBACILLUS RHAMNOSUS GG - P21212 SPACE GROUP WITH YB HEAVY ATOM
 
Authors :  P. Chaurasia, S. Pratap, I. Von Ossowski, A. Palva, V. Krishnan
Date :  21 Dec 15  (Deposition) - 20 Jul 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Pilin, Spaa, Probiotic, Isopeptide, Spacba Pili, Adhesin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Chaurasia, S. Pratap, I. Von Ossowski, A. Palva, V. Krishnan
New Insights About Pilus Formation In Gut-Adapted Lactobacillus Rhamnosus Gg From The Crystal Structure Of Th Spaa Backbone-Pilin Subunit
Sci Rep V. 6 28664 2016
PubMed-ID: 27349405  |  Reference-DOI: 10.1038/SREP28664

(-) Compounds

Molecule 1 - CELL SURFACE PROTEIN SPAA
    Atcc: 53103
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)/PLYSS
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN, RESIDUES 177-302
    Gene: LRHM_0426
    Organism Scientific: LACTOBACILLUS RHAMNOSUS GG
    Organism Taxid: 568703
    Strain: GG
    Synonym: PILUS PROTEIN SPAA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1YB10Ligand/IonYTTERBIUM (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1YB-1Ligand/IonYTTERBIUM (III) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1YB-1Ligand/IonYTTERBIUM (III) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1YB-1Ligand/IonYTTERBIUM (III) ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1YB-1Ligand/IonYTTERBIUM (III) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:204 , ASP A:283 , ASP C:277binding site for residue YB A 402
2AC2SOFTWARELYS A:185 , ASP A:292 , GLU C:191binding site for residue YB A 403
3AC3SOFTWAREASP A:277 , ASP C:283binding site for residue YB A 404
4AC4SOFTWARELYS B:185 , ASP B:292 , GLU D:191binding site for residue YB B 401
5AC5SOFTWAREASP A:277 , ASP C:283 , HOH C:501 , ASP D:204binding site for residue YB C 401
6AC6SOFTWAREASP B:212 , ASP B:214 , GLN B:216 , ASP C:214binding site for residue YB C 402
7AC7SOFTWAREASP A:283 , ASP C:277binding site for residue YB C 403
8AC8SOFTWAREASP B:204 , ASP B:283 , ASP D:277binding site for residue YB B 402
9AC9SOFTWAREASP B:277 , ASP C:204 , ASP D:283binding site for residue YB D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FGR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FGR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FGR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FGR)

(-) Exons   (0, 0)

(no "Exon" information available for 5FGR)

(-) 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:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeee.....eeeee............ee.......eeeeehhhhh..ee.....eeeeeee......eeeeeeeee........eee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgr A 177 TYERTFVKKDAETKEVLEGAGFKISNSDGKFLKLTDKDGQSVSIGEGFIDVLANNYRLTWVAESDATVFTSDKSGKFGLNGFADNTTTYTAVETNVPDGYDAAANTDFKADNSSSDILDAP 297
                                   186       196       206       216       226       236       246       256       266       276       286       296 


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..........eeeee.....eeeee............eehhhhhh.eeeeehhhhh..ee.....eeee.........eeeeeeeee........eee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgr B 178 YERTFVKKDAETKEVLEGAGFKISNSDGKFLKLTDKDGQSVSIGEGFIDVLANNYRLTWVAESDATVFTSDKSGKFGLNGFADNTTTYTAVETNVPDGYDAAANTDFKADNSSSDILDAPS 298
                                   187       197       207       217       227       237       247       257       267       277       287       297 


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeee.....eeeee............eehhhhhh.eeeeehhhhh..ee.....eeeeeee......eeeeeeeee........eee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgr C 177 TYERTFVKKDAETKEVLEGAGFKISNSDGKFLKLTDKDGQSVSIGEGFIDVLANNYRLTWVAESDATVFTSDKSGKFGLNGFADNTTTYTAVETNVPDGYDAAANTDFKADNSSSDILDAPS 298
                                   186       196       206       216       226       236       246       256       266       276       286       296  


Chain D from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeee.....eeeee............ee.......eeeeehhhhh..ee.....eeeeeee......eeeeeeeee........eee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgr D 177 TYERTFVKKDAETKEVLEGAGFKISNSDGKFLKLTDKDGQSVSIGEGFIDVLANNYRLTWVAESDATVFTSDKSGKFGLNGFADNTTTYTAVETNVPDGYDAAANTDFKADNSSSDILDAPS 298
                                   186       196       206       216       226       236       246       256       266       276       286       296
   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  (0, 0)

(no "SCOP Domain" information available for 5FGR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FGR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FGR)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/TrEMBL
        C7T9P4_LACRG | C7T9P4: 5f44 5faa 5fgs 5fie 5hbb 5hdl 5hts 5j4m

(-) Related Entries Specified in the PDB File

5f44 NEAR FULL-LENGTH OF SAME PROTEIN
5faa THE SAME PROTEIN IN I422 SPACE GROUP
5fgs THE SAME PROTEIN IN P21212 SPACE GROUP WITH ZN ION
5fie 5FIE CONTAINS N-TERMINAL DOMAIN OF THE SAME PROTEIN.
5hbb 5HBB CONTAINS E139A MUTANT OF THE SAME PROTEIN.
5hdl 5HDL CONTAINS E269A MUTANT OF THE SAME PROTEIN.
5hts 5HTS CONTAINS D295N MUTANT OF THE SAME PROTEIN.
5j4m 5J4M CONTAINS E269A/D295N MUTANT OF THE SAME PROTEIN.