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(-) Description

Title :  STRUCTURE OF THE SBSB S-LAYER PROTEIN OF GEOBACILLUS STEAROTHERMOPHILUS PV72P2 IN COMPLEX WITH NANOBODY KB6
 
Authors :  E. Baranova, H. Remaut
Date :  12 Apr 12  (Deposition) - 13 Jun 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A (1x),B (1x)
Biol. Unit 3:  C (1x),D (1x)
Biol. Unit 4:  C (1x),D (1x)
Keywords :  Structural Protein, S-Layer Protein, Nanobody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Baranova, R. Fronzes, A. Garcia-Pino, N. Van Gerven, D. Papapostolou, G. Pehau-Arnaudet, E. Pardon, J. Steyaert, S. Howorka, H. Remaut
Sbsb Structure And Lattice Reconstruction Unveil Ca21 Triggered S-Layer Assembly
Nature V. 487 119 2012
PubMed-ID: 22722836  |  Reference-DOI: 10.1038/NATURE11155

(-) Compounds

Molecule 1 - SBSB PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Variant: PLYSS
    Fragment: RESIDUES 32-920
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: PV72P2
 
Molecule 2 - SBSB PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Variant: PLYSS
    Fragment: RESIDUES 32-920
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: PV72P2
 
Molecule 3 - NBKB6
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector: PHEN6
    Expression System Vector Type: PLASMID
    Fragment: VHH
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:406 , THR A:440 , ASP A:779 , ASP A:781 , HOH A:2063BINDING SITE FOR RESIDUE CA A1923
2AC2SOFTWAREALA A:646 , THR A:649 , SER A:651 , ASP A:654 , HOH A:2153 , HOH A:2154BINDING SITE FOR RESIDUE CA A1924
3AC3SOFTWAREGLU A:784 , GLY A:822 , ASN A:824 , ASP A:835 , GLU A:836 , GLU A:837BINDING SITE FOR RESIDUE CA A1925
4AC4SOFTWAREASP A:517 , GLU A:518 , ASP A:592 , ASN A:624 , VAL A:625 , HOH A:2125BINDING SITE FOR RESIDUE CA A1926
5AC5SOFTWAREGLU C:784 , GLY C:822 , ASN C:824 , ASP C:835 , GLU C:836 , GLU C:837BINDING SITE FOR RESIDUE CA C1922
6AC6SOFTWAREGLN C:406 , THR C:440 , ASP C:779 , ASP C:781 , HOH C:2028BINDING SITE FOR RESIDUE CA C1923
7AC7SOFTWAREALA C:646 , THR C:649 , SER C:651 , ASP C:654 , HOH C:2092 , HOH C:2093BINDING SITE FOR RESIDUE CA C1924
8AC8SOFTWAREASP C:517 , GLU C:518 , ASP C:592 , ASN C:624 , VAL C:625 , HOH C:2072BINDING SITE FOR RESIDUE CA C1925

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:22 -B:96
2D:22 -D:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4AQ1)

(-) 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:721
 aligned with Q45664_GEOSE | Q45664 from UniProtKB/TrEMBL  Length:920

    Alignment length:721
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        920  
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       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       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911        |- 
         Q45664_GEOSE   202 AVPEIVEVTAVNSTTVKVTFNTQIADVDFTNFAIDNGLTVTKATLSRDKKSVEVVVNKPFTRNQEYTITATGIKNLKGETAKELTGKFVWSVQDAVTVALNNSSLKVGEESGLTVKDQDGKDVVGAKVELTSSNTNIVVVSSGEVSVSAAKVTAVKPGTADVTAKVTLPDGVVLTNTFKVTVTEVPVQVQNQGFTLVDNLSNAPQNTVAFNKAEKVTSMFAGETKTVAMYDTKNGDPETKPVDFKDATVRSLNPIIATAAINGSELLVTANAGQSGKASFEVTFKDNTKRTFTVDVKKDPVLQDIKVDATSVKLSDEAVGGGEVEGVNQKTIKVSAVDQYGKEIKFGTKGKVTVTTNTEGLVIKNVNSDNTIDFDSGNSATDQFVVVATKDKIVNGKVEVKYFKNASDTTPTSTKTITVNVVNVKADATPVGLDIVAPSEIDVNAPNTASTADVDFINFESVEIYTLDSNGNRLKKVTPTATTLVGTNDYVEVNGNVLQFKGNDELTLLTSSSTVNVDVTADGITKRIPVKYINSASVPASATVATSPVTVKLNSSDNDLTFEELIFGVIDPTQLVKDEDINEFIAVSKAAKNDGYLYNKPLVTVKDASGKVIPTGANVYGLNHDATNGNIWFDEEQAGLAKKFSDVHFDVDFSLANVVKTGSGTVSSSPSLSDAIQLTNSGDAVSFTLVIKSIYVKGADKDDNNLLAAPVSVNVTVTK--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeee.......hhh.eee.....eeeeee.....eeeeee........eeeeee.............eeeeee.......eeee...eee...ee.eeee..........eeeeee.....eee....ee.hhh.eee...eeeeeeeeee.....eeeeeeeeeee..........eeee.hhhhh..hhhhhhhh....eee...eeeeee..ee..ee..........eeee.....eeeeee..eeeeee.....eeeeeeee.....eeeeeeeee....eeeeee...eeeee.............eeeeeeeeee............eeeeee....eeee................eeeeeeee......eeeeeeeee.........eeeeeeeeee.........eeee....eee.hhhhh.......eee.hhh.eeee.....eeeee...eeee......eeee..eeee...hhhhhh...eeeeeeeee..eeeeeeeeee.....eeeeee....eeeee.....eeehhhhhhh..hhh.eeee....eeeee...............eeeee.......hhhhh..ee.........................eeeeeeeeeeeee.............eee......eeeeeeeeeeeee..............eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aq1 A 202 AVPEIVEVTAVNSTTVKVTFNTQIADVDFTNFAIDNGLTVTKATLSRDKKSVEVVVNKPFTRNQEYTITATGIKNLKGETAKELTGKFVWSVQDAVTVALNNSSLKVGEESGLTVKDQDGKDVVGAKVELTSSNTNIVVVSSGEVSVSAAKVTAVKPGTADVTAKVTLPDGVVLTNTFKVTVTEVPVQVQNQGFTLVDNLSNAPQNTVAFNKAEKVTSMFAGETKTVAMYDTKNGDPETKPVDFKDATVRSLNPIIATAAINGSELLVTANAGQSGKASFEVTFKDNTKRTFTVDVKKEPVLQDIKVDATSVKLSDEAVGGGEVEGVNQKTIKVSAVDQYGKEIKFGTKGKVTVTTNTEGLVIKNVNSDNTIDFDSGNSATDQFVVVATKDKIVNGKVEVKYFKNASDTTPTSTKTITVNVVNVKADATPVGLDIVAPSEIDVNAPNTASTADVDFINFESVEIYTLDSNGNRLKKVTPTATTLVGTNDYVEVNGNVLQFKGNDELTLLTSSSTVNVDVTADGITKRIPVKYINSASVPASATVATSPVTVKLNSSDNDLTFEELIFGVIDPTQLVKDEDINEFIAVSKAAKNDGYLYNKPLVTVKDASGEVIPTGANVYGLNHDATNGNIWFDEEQAGLAKKFSDVHFDVDFSLANVVKTGSGTVSSSPSLSDAIQLTNSGDAVSFTLVIKSIYVKGADKDDNNLLAAPVSVNVTVTKGS 922
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       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       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921 


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d4aq1b_ B: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee..hhhhheeeeeee......eeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeeee.......hhhhh.ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aq1 B   1 QVQLQESGGGLVQAGGSLRLSCAASGRTSSAYAMGWFRQAPGKEREFVAGISSKGGSTYYGASMKGRFTISRDNAKNTVYLQMNGLAPEDTAVYYCAASDKYNFDTSHAGYGYWGQGTQVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain C from PDB  Type:PROTEIN  Length:627
 aligned with Q45664_GEOSE | Q45664 from UniProtKB/TrEMBL  Length:920

    Alignment length:627
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           920 
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914     | 
         Q45664_GEOSE   295 DAVTVALNNSSLKVGEESGLTVKDQDGKDVVGAKVELTSSNTNIVVVSSGEVSVSAAKVTAVKPGTADVTAKVTLPDGVVLTNTFKVTVTEVPVQVQNQGFTLVDNLSNAPQNTVAFNKAEKVTSMFAGETKTVAMYDTKNGDPETKPVDFKDATVRSLNPIIATAAINGSELLVTANAGQSGKASFEVTFKDNTKRTFTVDVKKDPVLQDIKVDATSVKLSDEAVGGGEVEGVNQKTIKVSAVDQYGKEIKFGTKGKVTVTTNTEGLVIKNVNSDNTIDFDSGNSATDQFVVVATKDKIVNGKVEVKYFKNASDTTPTSTKTITVNVVNVKADATPVGLDIVAPSEIDVNAPNTASTADVDFINFESVEIYTLDSNGNRLKKVTPTATTLVGTNDYVEVNGNVLQFKGNDELTLLTSSSTVNVDVTADGITKRIPVKYINSASVPASATVATSPVTVKLNSSDNDLTFEELIFGVIDPTQLVKDEDINEFIAVSKAAKNDGYLYNKPLVTVKDASGKVIPTGANVYGLNHDATNGNIWFDEEQAGLAKKFSDVHFDVDFSLANVVKTGSGTVSSSPSLSDAIQLTNSGDAVSFTLVIKSIYVKGADKDDNNLLAAPVSVNVTVTK-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee...ee.eeee..........eeeeee.....eee...eee.....eee...eeeeeeeeee.....eeeeeeeeeee..........eeee.hhhhh..hhhhhhhh....eee...eeeeee..ee..ee..........eeee.....eeeeee..eeeeee.....eeeeeeee.....eeeeeeeee....eeeeee...eeeee.............eeeeeeeeee............eeeeee....eeee................eeeeeeee......eeeeeeeee.........eeeeeeeeee.........eeee....eee.hhhhh.......eee.hhh.eeee.....eeeee...eeee......eeee..eeee...hhhhhh...eeeeeeeee..eeeeeeeeee.......eeee....eeeee.....eeehhhhhhh..hhh.eeee....eeeee...............eeee........hhhhh.............................eeeeeeeeeeeee.............eee......eeeeeeeeeeeee..............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aq1 C 295 DAVTVALNNSSLKVGEESGLTVKDQDGKDVVGAKVELTSSNTNIVVVSSGEVSVSAAKVTAVKPGTADVTAKVTLPDGVVLTNTFKVTVTEVPVQVQNQGFTLVDNLTNAPQNTVAFNKAEKVTSMFAGETKTVAMYDTKNGDPETKPVDFKDATVRSLNPIIATAAINGSELLVTANAGQSGKASFEVTFKDNTKRTFTVDVKKEPVLQDIKVDATSVKLSDEAVGGGEVEGVNQKTIKVSAVDQYGKEIKFGTKGKVTVTTNTEGLVIKNVNSDNTIDFDSGNSATDQFVVVATKDKIVNGKVEVKYFKNASDTTPTSTKTITVNVVNVKADATPVGLDIVAPSEIDVNAPNTASTADVDFINFESVEIYTLDSNGNRLKKVTPTATTLVGTNDYVEVNGNVLQFKGNDELTLLTSSSTVNVDVTADGITKRIPVKYINSASVPASATVATSPVTVKLNSSDNDLTFEELIFGVIDPTQLVKDEDINEFIAVSKAAKNDGYLYNKPLVTVKDASGEVIPTGANVYGLNHDATNGNIWFDEEQAGLAKKFSDVHFDVDFSLANVVKTGSGTVSSSPSLSDAIQLTNSGDAVSFTLVIKSIYVKGADKDDNNLLAAPVSVNVTVTKG 921
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       


Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d4aq1d_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee..hhhhheeeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.......hhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aq1 D   1 QVQLQESGGGLVQAGGSLRLSCAASGRTSSAYAMGWFRQAPGKEREFVAGISSKGGSTYYGASMKGRFTISRDNAKNTVYLQMNGLAPEDTAVYYCAASDKYNFDTSHAGYGYWGQGTQVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AQ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AQ1)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q45664_GEOSE | Q45664)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  4aq1
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  Q45664_GEOSE | Q45664
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