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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA TOXIN FROM STAPHYLOCOCCUS AUREUS F277A, P278A MUTANT WITH BOUND MAGNESIUM IONS
 
Authors :  M. Huseby, K. Shi, A. C. Kruse, D. H. Ohlendorf
Date :  01 Jul 09  (Deposition) - 14 Jul 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Toxin, Hemolysin, Sphingomyelinase, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Huseby, K. Shi, A. C. Kruse, J. Digre, F. Mengistu, G. A. Bohach, P. S. Schlievert, D. H. Ohlendorf, C. A. Earhart
Structure And Biological Functions Of Beta Toxin From Staphylococcus Aureus: Role Of The Hydrophobic Beta Hairpin In Virulence
To Be Published 2009
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-HEMOLYSIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 35-330
    Gene: HLB
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS RN4220
    Organism Taxid: 561307
    Strain: RN2440

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:53 , PO4 A:403 , HOH A:464 , HOH A:465 , HOH A:466 , HOH A:467BINDING SITE FOR RESIDUE MG A 402
2AC2SOFTWAREASN A:16 , GLU A:53 , HIS A:150 , SER A:153 , ASP A:194 , ASN A:196 , HIS A:289 , MG A:402 , HOH A:464 , HOH A:465 , HOH A:466 , HOH A:495BINDING SITE FOR RESIDUE PO4 A 403
3AC3SOFTWAREGLU B:53 , PO4 B:404 , HOH B:460 , HOH B:461 , HOH B:462 , HOH B:463BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWAREASN B:16 , GLU B:53 , HIS B:150 , SER B:153 , ASP B:194 , ASN B:196 , HIS B:289 , HOH B:343 , MG B:401 , HOH B:462 , HOH B:463BINDING SITE FOR RESIDUE PO4 B 404

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:122 -A:158
2B:122 -B:158

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I48)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I48)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I48)

(-) Exons   (0, 0)

(no "Exon" information available for 3I48)

(-) 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:291
 aligned with A7LAI8_STAAU | A7LAI8 from UniProtKB/TrEMBL  Length:330

    Alignment length:291
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329 
         A7LAI8_STAAU    40 DTDLKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSGCGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKEISDFVKKKNIPKDETVYIGGDLNVNKGTPEFKDMLKNLNVNDVLYAGHNSTWDPQSNSIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAFPYYYVYNDFSDHYPIKAYSK 330
               SCOP domains d3i48a_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.........hhhhhhhhhhh........eeeeeee.hhhhhhhhhhhh.....ee............eeee............eeee...eeeeeeee.............eeeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhh....eeee.........hhhhhhhh........eeeee.........eeeee.......eeee....eeee........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i48 A   7 DTDLKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSGCGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKEISDFVKKKNIPKDETVYIGGDLNVNKGTPEFKDMLKNLNVNDVLYAGHNSTWDPQSNSIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAAAYYYVYNDFSDHYPIKAYSK 297
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with A7LAI8_STAAU | A7LAI8 from UniProtKB/TrEMBL  Length:330

    Alignment length:290
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
         A7LAI8_STAAU    41 TDLKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSGCGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKEISDFVKKKNIPKDETVYIGGDLNVNKGTPEFKDMLKNLNVNDVLYAGHNSTWDPQSNSIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAFPYYYVYNDFSDHYPIKAYSK 330
               SCOP domains d3i48b_ B: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.........hhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhh....ee............eeee............eeee...eeeeeeee....hhhhhhh..eeeeeeeee..eeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh.......eeeeee......hhhhhhhhhhhh....eeee.........hhhhhhhh........eeeee.........eeeee.......eeee....eeee........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i48 B   8 TDLKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSGCGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKEISDFVKKKNIPKDETVYIGGDLNVNKGTPEFKDMLKNLNVNDVLYAGHNSTWDPQSNSIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAAAYYYVYNDFSDHYPIKAYSK 297
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I48)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I48)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A7LAI8_STAAU | A7LAI8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
cellular component
    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

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

UniProtKB/Swiss-Prot
        A7LAI8_STAAU | A7LAI8: 3i5v
UniProtKB/TrEMBL
        A7LAI8_STAAU | A7LAI8: 3i41 3i46 3k55

(-) Related Entries Specified in the PDB File

3i41 CRYSTAL STRUCTURE OF BETA TOXIN FROM STAPHYLOCOCCUS AUREUS F277A, P278A MUTANT
3i46 CRYSTAL STRUCTURE OF BETA TOXIN FROM STAPHYLOCOCCUS AUREUS F277A, P278A MUTANT WITH BOUND CALCIUM IONS
3i5v CRYSTAL STRUCTURE OF BETA TOXIN 275-280 DELETION MUTANT FROM STAPHYLOCOCCUS AUREUS