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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VARIABLE DOMAIN OF THE STREPTOCOCCUS GORDONII SURFACE PROTEIN SSPB
 
Authors :  N. Forsgren, K. Persson
Date :  20 Mar 09  (Deposition) - 28 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Cell Adhesion, Secreted, V-Region, Cell Wall, Ag I/Ii Protein, Surface Adhesin, Peptidoglycan-Anchor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Forsgren, R. J. Lamont, K. Persson
Crystal Structure Of The Variable Domain Of The Streptococcus Gordonii Surface Protein Sspb.
Protein Sci. V. 18 1896 2009
PubMed-ID: 19609934  |  Reference-DOI: 10.1002/PRO.200

(-) Compounds

Molecule 1 - AGGLUTININ RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-VECTOR
    Fragment: VARIABLE DOMAIN, RESIDUES 449-797
    Organism Scientific: STREPTOCOCCUS GORDONII
    Organism Taxid: 1302
    Strain: M5
    Synonym: SSP-5, CELL SURFACE ANTIGEN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:711 , THR A:712 , THR B:711 , THR B:712BINDING SITE FOR RESIDUE K B1762
2AC2SOFTWARESER A:648 , ASN A:650 , GLU A:664 , HOH A:2088 , HOH A:2100 , HOH A:2159BINDING SITE FOR RESIDUE CA A1765
3AC3SOFTWARESER B:648 , ASN B:650 , GLU B:664 , HOH B:2054 , HOH B:2057 , HOH B:2098BINDING SITE FOR RESIDUE CA B1763
4AC4SOFTWARESER A:541 , TYR A:542 , ALA A:545 , TRP B:704 , ASN B:716 , GOL B:1765BINDING SITE FOR RESIDUE GOL B1764
5AC5SOFTWARETRP A:704 , ASN A:716 , GOL A:1767 , ALA B:545BINDING SITE FOR RESIDUE GOL A1766
6AC6SOFTWARETYR A:542 , TRP A:613 , ASN A:742 , GLU B:708 , SER B:714 , PRO B:715 , GOL B:1764 , HOH B:2085BINDING SITE FOR RESIDUE GOL B1765
7AC7SOFTWAREGLU A:708 , SER A:714 , GOL A:1766 , TYR B:542 , TRP B:613 , ASN B:742BINDING SITE FOR RESIDUE GOL A1767

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WD6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WD6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WD6)

(-) Exons   (0, 0)

(no "Exon" information available for 2WD6)

(-) 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:302
 aligned with SSP5_STRGN | P16952 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:302
                                   471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761  
           SSP5_STRGN   462 YKKEFAAYTAALAEAESKKKQDGYLSEPRSQSLNFKSEPNAIRTIDSSVHQYGQQELDALVKSWGISPTNPDRKKSRAYSYFNAINSNNTYAKLVLEKDKPVDVTYTGLKNSSFNGKKISKVVYTYTLKETGFNDGTKMTMFASSDPTVTAWYNDYFTSTNINVKVKFYDEEGQLMNLTGGLVNFSSLNRGNGSGAIDKDAIESVRNFNGRYIPISGSSIKIHENNSAYADSSNAEKSLGARWNTSEWDTTSSPNNWYGAIVGEITQSEISFNMASSKSGNIWFAFNSNINAIGVPTKPVAP 763
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..............ee.......eee........hhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....eeeeee....eeeeee.....ee..ee..eeeeeeeeeee......eeeeee.......eeee....eeeeeeeeeee.....ee.....eeee................eeeee....eee......eeee...eeee.....hhhhh...hhhhh......hhhhhheeee....eeeeeeeee...eeee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wd6 A 462 YKKEFAAYTAALAEAESKKKQDGYLSEPRSQSLNFKSEPNAIRTIDSSVHQYGQQELDALVKSWGISPTNPDRKKSRAYSYFNAINSNNTYAKLVLEKDKPVDVTYTGLKNSSFNGKKISKVVYTYTLKETGFNDGTKMTMFASSDPTVTAWYNDYFTSTNINVKVKFYDEEGQLMNLTGGLVNFSSLNRGNGSGAIDKDAIESVRNFNGRYIPISGSSIKIHENNSAYADSSNAEKSLGARWNTSEWDTTSSPNNWYGAIVGEITQSEISFNMASSKSGNIWFAFNSNINAIGVPTKPVAP 763
                                   471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761  


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with SSP5_STRGN | P16952 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:293
                                   477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757   
           SSP5_STRGN   468 AYTAALAEAESKKKQDGYLSEPRSQSLNFKSEPNAIRTIDSSVHQYGQQELDALVKSWGISPTNPDRKKSRAYSYFNAINSNNTYAKLVLEKDKPVDVTYTGLKNSSFNGKKISKVVYTYTLKETGFNDGTKMTMFASSDPTVTAWYNDYFTSTNINVKVKFYDEEGQLMNLTGGLVNFSSLNRGNGSGAIDKDAIESVRNFNGRYIPISGSSIKIHENNSAYADSSNAEKSLGARWNTSEWDTTSSPNNWYGAIVGEITQSEISFNMASSKSGNIWFAFNSNINAIGVPTKP 760
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Str------GbpC-2wd6B01 B:477-748                                                                                                                                                                                                                                                          ------------ Pfam domains (1)
           Pfam domains (2) Str------GbpC-2wd6B02 B:477-748                                                                                                                                                                                                                                                          ------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh..............ee.......eee........hhhhhhhhhhh........hhhhhhhhhhhhhhh.....eeeeee....eeeeee.....ee..ee..eeeeeeeeeee......eeeeee.......eeee....eeeeeeeeeee............eeee................eeeee....eee......eeee...eeee.....hhhhh...hhhhh......hhhhhheeee.....eeeeeeee...eeee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wd6 B 468 AYTAALAEAESKKKQDGYLSEPRSQSLNFKSEPNAIRTIDSSVHQYGQQELDALVKSWGISPTNPDRKKSRAYSYFNAINSNNTYAKLVLEKDKPVDVTYTGLKNSSFNGKKISKVVYTYTLKETGFNDGTKMTMFASSDPTVTAWYNDYFTSTNINVKVKFYDEEGQLMNLTGGLVNFSSLNRGNGSGAIDKDAIESVRNFNGRYIPISGSSIKIHENNSAYADSSNAEKSLGARWNTSEWDTTSSPNNWYGAIVGEITQSEISFNMASSKSGNIWFAFNSNINAIGVPTKP 760
                                   477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757
   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 2WD6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WD6)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: GbpC] (1)
(-)
Clan: no clan defined [family: Strep_SA_rep] (1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SSP5_STRGN | P16952)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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

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UniProtKB/Swiss-Prot
        SSP5_STRGN | P16952: 2woy 2wqs 2wza

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