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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE STREPTOCOCCUS GORDONII ADHESIN SGO0707
 
Authors :  A. Nylander, G. Svensater, D. B. Senadheera, D. G. Cvitkovitch, J. R. Da K. Persson
Date :  17 Dec 12  (Deposition) - 05 Jun 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
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 :  Beta-Sandwich Folds, Adhesin, Collagen-Binding, Oral Keratinocytes, Cell Wall Anchored Protein, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Nylander, G. Svensater, D. B. Senadheera, D. G. Cvitkovitch, J. R. Davies, K. Persson
Structural And Functional Analysis Of The N-Terminal Domain Of The Streptococcus Gordonii Adhesin Sgo0707
Plos One V. 8 63768 2013
PubMed-ID: 23691093  |  Reference-DOI: 10.1371/JOURNAL.PONE.0063768

(-) Compounds

Molecule 1 - LPXTG CELL WALL SURFACE PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSGO0707-N, UNP RESIDUES 36-458
    GeneSGO_0707
    Organism ScientificSTREPTOCOCCUS GORDONII
    Organism Taxid29390
    StrainCHALLIS / ATCC 35105 / CH1 / DL1 / V288
 
Molecule 2 - LPXTG CELL WALL SURFACE PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSGO_0707
    Organism ScientificSTREPTOCOCCUS GORDONII
    Organism Taxid29390
    StrainCHALLIS / ATCC 35105 / CH1 / DL1 / V288
 
Molecule 3 - LPXTG CELL WALL SURFACE PROTEIN
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSGO_0707
    Organism ScientificSTREPTOCOCCUS GORDONII
    Organism Taxid29390
    StrainCHALLIS / ATCC 35105 / CH1 / DL1 / V288
 
Molecule 4 - LPXTG CELL WALL SURFACE PROTEIN
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSGO_0707
    Organism ScientificSTREPTOCOCCUS GORDONII
    Organism Taxid29390
    StrainCHALLIS / ATCC 35105 / CH1 / DL1 / V288

 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  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:53 , GLU A:169 , LYS A:218 , TYR A:309 , HOH A:783 , HOH A:820 , HOH A:877 , HOH A:882 , HOH A:969BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREASP A:221 , ASP A:223 , NA A:505 , HOH A:802 , HOH A:825 , HOH A:1003BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREASN A:124 , ILE A:310 , GLU A:311 , LYS A:312 , ILE A:313 , SER A:444 , HOH A:626 , HOH A:962BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWARESER A:65 , SER A:114 , ASN A:133 , LEU B:64 , TYR B:131 , ARG B:204 , HOH B:922BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREASP A:221 , ASP A:223 , THR A:271 , SO4 A:502 , HOH A:1001 , HOH A:1003BINDING SITE FOR RESIDUE NA A 505
06AC6SOFTWARELYS B:53 , GLU B:169 , LYS B:218 , TYR B:309 , HOH B:792BINDING SITE FOR RESIDUE SO4 B 501
07AC7SOFTWAREASP B:221 , ASP B:223 , NA B:504 , HOH B:778 , HOH B:847BINDING SITE FOR RESIDUE SO4 B 502
08AC8SOFTWAREASN B:124 , ILE B:310 , GLU B:311 , ILE B:313 , SER B:444 , HOH B:617BINDING SITE FOR RESIDUE GOL B 503
09AC9SOFTWAREASP B:221 , ASP B:223 , THR B:271 , SO4 B:502 , HOH B:950BINDING SITE FOR RESIDUE NA B 504
10BC1SOFTWARELYS C:53 , TYR C:309 , HOH C:716 , HOH C:778BINDING SITE FOR RESIDUE SO4 C 501
11BC2SOFTWAREASP C:221 , ASP C:223 , NA C:505 , HOH C:866BINDING SITE FOR RESIDUE SO4 C 502
12BC3SOFTWAREASN C:124 , GLU C:311 , ILE C:313 , ARG C:316 , SER C:444 , ALA C:445BINDING SITE FOR RESIDUE GOL C 503
13BC4SOFTWARETYR C:80 , TRP C:168 , SER C:303 , HOH C:757BINDING SITE FOR RESIDUE ACT C 504
14BC5SOFTWAREASP C:221 , ASP C:223 , THR C:271 , GLU C:277 , SO4 C:502BINDING SITE FOR RESIDUE NA C 505
15BC6SOFTWARELYS D:53 , LYS D:218 , TYR D:309 , HOH D:748 , HOH D:810BINDING SITE FOR RESIDUE SO4 D 501
16BC7SOFTWAREASP D:221 , ASP D:223 , NA D:504 , HOH D:648 , HOH D:855BINDING SITE FOR RESIDUE SO4 D 502
17BC8SOFTWAREASN D:124 , GLU D:311 , LYS D:312 , ILE D:313 , ARG D:316 , SER D:444BINDING SITE FOR RESIDUE GOL D 503
18BC9SOFTWAREASP D:221 , GLU D:232 , SER D:303 , SO4 D:502BINDING SITE FOR RESIDUE NA D 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Asp A:314 -Pro A:315
2Asp A:322 -Pro A:323
3Pro B:89 -Gly B:90
4Asp B:314 -Pro B:315
5Asp B:322 -Pro B:323
6Lys B:427 -Gly B:428
7Ser B:429 -Glu B:430
8Asp C:314 -Pro C:315
9Asp C:322 -Pro C:323
10Asp D:314 -Pro D:315
11Asp D:322 -Pro D:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IGB)

(-) 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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee..hhhhh..ee.......eeeeee...eeeeeee..ee..........eeeeeeee........eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee..hhhhhhhhhh....eeeeeeee......eeeee...ee...........eeeeeeeeeeeee..........ee...............eeeeehhhhheeeeeee.....eeee...eeeee......hhhhhhhh...eeee...eeeeeee.....eeee..ee.......eeeee..eee.....eeeeeeee...............eeeeee....eeeeeeeeee..ee......eeeeee..eeeeeehhhhhhh.....eeeeeeeee........eeee.eeeee..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4igb A  -6 LYFQGAMALEEIKNGTDISTLDIRKFNLNINNVSVLSKSQSVDQFHLSNPHYEYLSGGAYPGEMENFTLKVDKSKKQDQVFENPLSLKFTNIGTVNGKQVDAYLNFNKVTLHYLNTAQAESEMNSAQKSTVEFFSISELWESNAFEIGNVPYVDANHDYIMNKAFWIDADVTAEIRYADGTETDLKLVMKPTDIDAIDANNLKETFYVKNYQNDVNLRLMNNANVLVQEEASDRTSWIATQITGGSYNENNVSGLALRSNSNSMNFGYSSTETCSAVFGLYIEKIDPRPVLEVDPAEIPAKDGQDVTYKATFKVPVPGKDILAAPSSIEMVQKFDERLDYKELKVESGGVTLQEGRDYTIEKTGQTVTVKMTPEYLKGNSSSDIIITYKTATNKKVEESEKIDNTVTLHVDNLSAPSNQVSTALLY 456
                                  ||38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       430       440       450      
                                  0|                                                                                                                                                                                                                                                                                                                                                                                                   426|                           
                                  36                                                                                                                                                                                                                                                                                                                                                                                                    429                           

Chain B from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee..hhhhh..ee.......eeeeee...eeeeeee..ee..........eeeeeeee........eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee..hhhhhhhhhh....eeeeeeee......eeeee...ee...........eeeeeeeeeeeee..........ee...............eeeeehhhhheeeeeee.....eeee...eeeee.....hhhhhhhhh...eeee...eeeeeee.....eeee..ee.......eeeee..eee.....eeeeeeee...............eeeeee....eeeeeeeeee..ee......eeeeee..eeeeeehhhhhhh.....eeeeeeeee.hhhhh.....eee.eeeee..eeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4igb B -11 PTTENLYFQGAMALEEIKNGTDISTLDIRKFNLNINNVSVLSKSQSVDQFHLSNPHYEYLSGGAYPGEMENFTLKVDKSKKQDQVFENPLSLKFTNIGTVNGKQVDAYLNFNKVTLHYLNTAQAESEMNSAQKSTVEFFSISELWESNAFEIGNVPYVDANHDYIMNKAFWIDADVTAEIRYADGTETDLKLVMKPTDIDAIDANNLKETFYVKNYQNDVNLRLMNNANVLVQEEASDRTSWIATQITGGSYNENNVSGLALRSNSNSMNFGYSSTETCSAVFGLYIEKIDPRPVLEVDPAEIPAKDGQDVTYKATFKVPVPGKDILAAPSSIEMVQKFDERLDYKELKVESGGVTLQEGRDYTIEKTGQTVTVKMTPEYLKGNSSSDIIITYKTATNKKVEEKGSEKIDNTVTLHVDNLSAPSNQVSTALLYEK 458
                                    -2 ||     43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453     
                                       0|                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                       36                                                                                                                                                                                                                                                                                                                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeeeee..hhhhh..ee.......eeeeee...eeeeeee..ee..........eeeeeeee........eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee..hhhhhhhhhh....eeeeeeee......eeeee...ee...........eeeeeeeeeeeee..........ee...............eeeeehhhhheeeeeee.....eeee...eeeee......hhhhhhhh...eeee...eeeeeee.....eeee..ee.......eeeee..eee.....eeeeeeee...............eeeeee....eeeeeeeeee..ee......eeeeee..eeeeeehhhhhh......eeeeeeeee.hhhhh....eeee.eeeee..eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4igb C -12 IPTTENLYFQGAMALEEIKNGTDISTLDIRKFNLNINNVSVLSKSQSVDQFHLSNPHYEYLSGGAYPGEMENFTLKVDKSKKQDQVFENPLSLKFTNIGTVNGKQVDAYLNFNKVTLHYLNTAQAESEMNSAQKSTVEFFSISELWESNAFEIGNVPYVDANHDYIMNKAFWIDADVTAEIRYADGTETDLKLVMKPTDIDAIDANNLKETFYVKNYQNDVNLRLMNNANVLVQEEASDRTSWIATQITGGSYNENNVSGLALRSNSNSMNFGYSSTETCSAVFGLYIEKIDPRPVLEVDPAEIPAKDGQDVTYKATFKVPVPGKDILAAPSSIEMVQKFDERLDYKELKVESGGVTLQEGRDYTIEKTGQTVTVKMTPEYLKGNSSSDIIITYKTATNKKVEEKGSEKIDNTVTLHVDNLSAPSNQVSTALL 455
                                    -3  ||    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   
                                        0|                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                        36                                                                                                                                                                                                                                                                                                                                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..ee.......eeeeee...eeeeeee..ee..........eeeeeeee........eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee..hhhhhhhhhh....eeeeeeee......eeeee...eehhhhh......eeeeeeeeeeeee..........ee...............eeeeehhhhheeeeeee.....eeee...eeeee......hhhhhhhh...eeee...eeeeeee.....eeee..ee.......eeeee..ee......eeeeeeee...............eeeeee....eeeeeeeee...........eeeeee..eeeeeehhhhhhhh....eeeeeeeee.hhhh..eee.eeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4igb D  36 ALEEIKNGTDISTLDIRKFNLNINNVSVLSKSQSVDQFHLSNPHYEYLSGGAYPGEMENFTLKVDKSKKQDQVFENPLSLKFTNIGTVNGKQVDAYLNFNKVTLHYLNTAQAESEMNSAQKSTVEFFSISELWESNAFEIGNVPYVDANHDYIMNKAFWIDADVTAEIRYADGTETDLKLVMKPTDIDAIDANNLKETFYVKNYQNDVNLRLMNNANVLVQEEASDRTSWIATQITGGSYNENNVSGLALRSNSNSMNFGYSSTETCSAVFGLYIEKIDPRPVLEVDPAEIPAKDGQDVTYKATFKVPVPGKDILAAPSSIEMVQKFDERLDYKELKVESGGVTLQEGRDYTIEKTGQTVTVKMTPEYLKGNSSSDIIITYKTATNKKVEEKIDNTVTLHVDNLSAPSNQVSTALL 455
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425||     439       449      
                                                                                                                                                                                                                                                                                                                                                                                                                                426|                        
                                                                                                                                                                                                                                                                                                                                                                                                                                 431                        

   Legend:   → Mismatch (orange background)
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    → 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 4IGB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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