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(-) Description

Title :  CRYSTAL STRUCTURE OF RHIZAVIDIN-BIOTIN COMPLEX
 
Authors :  O. Livnah, A. Meir
Date :  14 Oct 08  (Deposition) - 23 Dec 08  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (2x)
Biol. Unit 4:  F,G  (1x)
Keywords :  High Affinity, Rhizavidin, Biotin, Avidin, Streptavidin, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Meir, S. H. Helppolainen, E. Podoly, H. R. Nordlund, V. P. Hytonen, J. A. Maatta, M. Wilchek, E. A. Bayer, M. S. Kulomaa, O. Livnah
Crystal Structure Of Rhizavidin: Insights Into The Enigmatic High-Affinity Interaction Of An Innate Biotin-Binding Protein Dimer.
J. Mol. Biol. V. 386 379 2009
PubMed-ID: 19111749  |  Reference-DOI: 10.1016/J.JMB.2008.11.061
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHIZAVIDIN
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHE_PD00032
    Organism Scientific: RHIZOBIUM ETLI
    Organism Taxid: 347834
    Strain: CFN 42

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): AB     
Biological Unit 2 (1x):   CD   
Biological Unit 3 (2x):     E  
Biological Unit 4 (1x):      FG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1BTN7Ligand/IonBIOTIN
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BTN2Ligand/IonBIOTIN
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BTN2Ligand/IonBIOTIN
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1BTN2Ligand/IonBIOTIN
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1BTN2Ligand/IonBIOTIN

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:21 , SER A:25 , TYR A:41 , ASN A:43 , ALA A:45 , GLY A:49 , TRP A:72 , SER A:81 , THR A:83 , TRP A:102 , ASP A:119 , GLY G:247BINDING SITE FOR RESIDUE BTN A 400
2AC2SOFTWAREASN B:221 , SER B:225 , TYR B:241 , ASN B:243 , ALA B:245 , THR B:248 , GLY B:249 , TRP B:272 , CYS B:279 , SER B:281 , THR B:283 , TRP B:302 , ASP B:319 , SER F:131BINDING SITE FOR RESIDUE BTN B 500
3AC3SOFTWAREASN C:21 , SER C:25 , TYR C:41 , ASN C:43 , ALA C:45 , GLY C:49 , TRP C:72 , SER C:81 , THR C:83 , TRP C:102 , LEU C:104 , ASP C:119BINDING SITE FOR RESIDUE BTN C 600
4AC4SOFTWAREGLY D:224 , TYR D:241 , ASN D:243 , THR D:248 , TRP D:272 , CYS D:279 , SER D:281 , THR D:283 , TRP D:285 , TRP D:302 , ASP D:319BINDING SITE FOR RESIDUE BTN D 700
5AC5SOFTWAREASN E:21 , SER E:25 , TYR E:41 , ASN E:43 , ALA E:45 , THR E:48 , GLY E:49 , TRP E:72 , CYS E:79 , SER E:81 , THR E:83 , TRP E:102 , ASP E:119BINDING SITE FOR RESIDUE BTN E 800
6AC6SOFTWAREASN F:21 , SER F:25 , TYR F:41 , ASN F:43 , ALA F:45 , THR F:48 , GLY F:49 , TRP F:72 , CYS F:79 , SER F:81 , THR F:83 , TRP F:85 , TRP F:102 , ASP F:119BINDING SITE FOR RESIDUE BTN F 900
7AC7SOFTWAREGLY A:47 , ASN G:221 , SER G:225 , TYR G:241 , ASN G:243 , ALA G:245 , THR G:248 , GLY G:249 , TRP G:272 , CYS G:279 , SER G:281 , THR G:283 , TRP G:302 , ASP G:319BINDING SITE FOR RESIDUE BTN G 350

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:50 -A:79
2B:250 -B:279
3C:50 -C:79
4D:250 -D:279
5E:50 -E:79
6F:50 -F:79
7G:250 -G:279

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EW2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EW2)

(-) Exons   (0, 0)

(no "Exon" information available for 3EW2)

(-) 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:114
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:114
                                    44        54        64        74        84        94       104       114       124       134       144    
         Q8KKW2_RHIEC    35 ASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 148
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3ew2 A  15 ASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 128
                                    24        34        44        54        64        74        84        94       104       114       124    


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:121
                                    37        47        57        67        77        87        97       107       117       127       137       147 
         Q8KKW2_RHIEC    28 DFSSIASASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 148
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee...eeeeeeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ew2 B 208 DFSSIASASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 328
                                   217       227       237       247       257       267       277       287       297       307       317       327 


Chain C from PDB  Type:PROTEIN  Length:124
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:124
                                    34        44        54        64        74        84        94       104       114       124       134       144    
         Q8KKW2_RHIEC    25 NFKDFSSIASASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeee....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeeee..eeeeeee..eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ew2 C   5 NFKDFSSIASASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 128
                                    14        24        34        44        54        64        74        84        94       104       114       124    


Chain D from PDB  Type:PROTEIN  Length:95
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:104
                                    47        57        67        77        87        97       107       117       127       137    
         Q8KKW2_RHIEC    38 SWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTF 141
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-...eeeeee....eeeeeee............eeeeeeee..eeeeeee..........eeeeeee.--------....eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3ew2 D 218 SWQN-SGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYA--------IVTSWNLAYEGGSGPAIEQGQDTF 321
                               | | 227       237       247       257       267       277       287 |       -|      307       317    
                             221 |                                                               289      298                       
                               223                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:119
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:119
                                    39        49        59        69        79        89        99       109       119       129       139         
         Q8KKW2_RHIEC    30 SSIASASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 148
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3ew2 E  10 SSIASASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTE 128
                                    19        29        39        49        59        69        79        89        99       109       119         


Chain F from PDB  Type:PROTEIN  Length:119
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:121
                                    43        53        63        73        83        93       103       113       123       133       143       153 
         Q8KKW2_RHIEC    34 SASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTENKSLLK 154
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeeee...eeeeeee............eeeeeeee..eeeeeeeee....eeeeeeeeeeeeee.-..eeeeeeeeeeeee..ee..eee..eeeee..ee....-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ew2 F  14 SASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVN-NNTEIVTSWNLAYEGGSGPAIEQGQDTFQYVPTTENKSL-K 134
                                    23        33        43        53        63        73        83        |-|      103       113       123        |-|
                                                                                                         92 |                                   132 |
                                                                                                           94                                     134


Chain G from PDB  Type:PROTEIN  Length:110
 aligned with Q8KKW2_RHIEC | Q8KKW2 from UniProtKB/TrEMBL  Length:155

    Alignment length:110
                                    44        54        64        74        84        94       104       114       124       134       144
         Q8KKW2_RHIEC    35 ASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYV 144
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee....eeeeeeeeeeeee......eeeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3ew2 G 215 ASSSWQNQSGSTMIIQVDSFGNVSGQYVNRAQGTGCQNSPYPLTGRVNGTFIAFSVGWNNSTENCNSATGWTGYAQVNGNNTEIVTSWNLAYEGGSGPAIEQGQDTFQYV 324
                                   224       234       244       254       264       274       284       294       304       314       324
   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 3EW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EW2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3EW2)

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 Related Entries

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

UniProtKB/TrEMBL
        Q8KKW2_RHIEC | Q8KKW2: 3ew1

(-) Related Entries Specified in the PDB File

3ew1