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(-) Description

Title :  STRUCTURE OF THE N248A MUTANT OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
 
Authors :  L. Maveyraud, B. J. Laventie, G. Prevost, L. Mourey
Date :  30 Jan 13  (Deposition) - 29 Jan 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
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 :  Bi-Component Leucotoxin, Staphylococcus Aureus, S Component Leucocidin, Beta-Barrel Pore Forming Toxin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Laventie, F. Guerin, L. Mourey, M. Y. Tawk, E. Jover, L. Maveyraud G. Prevost
Residues Essential For Panton-Valentine Leukocidin S Component Binding To Its Cell Receptor Suggest Both Plasticity And Adaptability In Its Interaction Surface
Plos One V. 9 92094 2014
PubMed-ID: 24643034  |  Reference-DOI: 10.1371/JOURNAL.PONE.0092094
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUKS-PV
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 29-312
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS PHAGE PVL
    Organism Taxid: 71366

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4IZL)

(-) Sites  (0, 0)

(no "Site" information available for 4IZL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:95 -Pro A:96
2Arg A:242 -Thr A:243
3Leu B:95 -Pro B:96
4Thr B:243 -Thr B:244
5Leu C:95 -Pro C:96
6Leu D:95 -Pro D:96
7Gly D:180 -Tyr D:181
8Tyr D:246 -Gly D:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IZL)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4izla_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee...eeee......eeeeeeeeeeeeeeee....eeeeeee........eeeeeeeee...eeeee.......eeeeeeee...eeeeeeee...eeeeeeee.eeee..eeee...............hhhhhh.hhhhhhhhhhhee..eeeeeeeee.....eeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izl A   2 NNIENIGDGAEVVKRTEDTSSDKWGVTQNIQFDFVKDKKYNKDALILKMQGFINSKTTYYNYKNTDHIKAMRWPFQYNIGLKTNDPNVDLINYLPKNKIDSVNVSQTLGYNIGGNFNSGPSNGSFNYSKTISYNQQNYISEVEHQNSKSVQWGIKANSFITSLGKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFEITYGRNMDVTHATRRTTHYGASYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN 284
                                    11        21        31        41        51        61        71        81        91       101       111       121||     134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284
                                                                                                                                                  122|                                                                                                                                                              
                                                                                                                                                   126                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4izlb_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee...eeee......eeeeeeeeeeeeeeee....eeeeeee........eeeeeeeee...eeeee.....eeeeeeee...eeeeeeee...eeeeeeee.eeee..eeee...............hhhhhh.hhhhhhhhhhhee..eeeeeeeee.....eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izl B   2 NNIENIGDGAEVVKRTEDTSSDKWGVTQNIQFDFVKDKKYNKDALILKMQGFINSKTTYYNYKNTDHIKAMRWPFQYNIGLKTNDPNVDLINYLPKNKIDSVNVSQTLGYNIGGNFNSGPSSFNYSKTISYNQQNYISEVEHQNSKSVQWGIKANSFITSLGKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFEITYGRNMDVTHATRRTTHYGASYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN 284
                                    11        21        31        41        51        61        71        81        91       101       111       121||     136       146       156       166       176       186       196       206       216       226       236       246       256       266       276        
                                                                                                                                                  122|                                                                                                                                                            
                                                                                                                                                   128                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4izlc_ C: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee...eeee......eeeeeeeeeeeeeeee....eeeeeee...ee...eeeeeeeee...eeeeee.....eeeeeeee...eeeeeeee...eeeeeeee.eeee..eeee...............hhhhhh.hhhhhhhhhhhee..eeeeeeeee.....eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izl C   3 NIENIGDGAEVVKRTEDTSSDKWGVTQNIQFDFVKDKKYNKDALILKMQGFINSKTTYYNYKNTDHIKAMRWPFQYNIGLKTNDPNVDLINYLPKNKIDSVNVSQTLGYNIGGNFNSGPSTSFNYSKTISYNQQNYISEVEHQNSKSVQWGIKANSFITSLGKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFEITYGRNMDVTHATRRTTHYGASYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN 284
                                    12        22        32        42        52        62        72        82        92       102       112       122||     136       146       156       166       176       186       196       206       216       226       236       246       256       266       276        
                                                                                                                                                  123|                                                                                                                                                            
                                                                                                                                                   128                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4izld_ D: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee...eeee......eeeeeeeeeeeeeeee....eeeeeee........eeeeeeeee...eee......eeeeeeee...eeeeeeee...eeeeeeee.eeee..eeee...............hhhhhh.hhhhhhhhhhhee..eeeeeeeee.....eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izl D   2 NNIENIGDGAEVVKRTEDTSSDKWGVTQNIQFDFVKDKKYNKDALILKMQGFINSKTTYYNYKNTDHIKAMRWPFQYNIGLKTNDPNVDLINYLPKNKIDSVNVSQTLGYNIGGNFNSNGSFNYSKTISYNQQNYISEVEHQNSKSVQWGIKANSFITSLGKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFEITYGRNMDVTHATRRTTHYGASYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN 284
                                    11        21        31        41        51        61        71        81        91       101       111       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       
                                                                                                                                               119|                                                                                                                                                              
                                                                                                                                                126
   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, 4)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:242 - Thr A:243   [ RasMol ]  
    Gly D:180 - Tyr D:181   [ RasMol ]  
    Leu A:95 - Pro A:96   [ RasMol ]  
    Leu B:95 - Pro B:96   [ RasMol ]  
    Leu C:95 - Pro C:96   [ RasMol ]  
    Leu D:95 - Pro D:96   [ RasMol ]  
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    Tyr D:246 - Gly D:247   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        O80066_9CAUD | O80066: 1t5r
UniProtKB/TrEMBL
        O80066_9CAUD | O80066: 4iya 4iyc 4iyt 4j0o

(-) Related Entries Specified in the PDB File

1pvl STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN F COMPONENT FROM STAPHYLOCOCCUS AUREUS
1t5r STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
4iya STRUCTURE OF THE Y250A MUTANT OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
4iyc STRUCTURE OF THE T244A MUTANT OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
4iyt STRUCTURE OF THE Y184A MUTANT OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
4j0o STRUCTURE OF THE Y246A MUTANT OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS