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(-) Description

Title :  CLYA CC6/264 OX (6-303)
 
Authors :  D. J. A. Roderer, R. Glockshuber, N. Ban
Date :  06 May 14  (Deposition) - 24 Sep 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
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 :  Alpha Pore-Forming Toxin, Intramolecular Disulfide Bond, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Roderer, S. Benke, M. Muller, H. Fah-Rechsteiner, N. Ban, B. Schuler, R. Glockshuber
Characterization Of Variants Of The Pore-Forming Toxin Clya From Escherichia Coli Controlled By A Redox Switch.
Biochemistry V. 53 6357 2014
PubMed-ID: 25222267  |  Reference-DOI: 10.1021/BI5007578

(-) Compounds

Molecule 1 - HEMOLYSIN E, CHROMOSOMAL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: TUNER
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HLYE, CLYA, HPR, SHEA, YCGD, B1182, JW5181
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CYTOTOXIN CLYA,HEMOLYSIS-INDUCING PROTEIN,LATENT PORE- FORMING 34 KDA HEMOLYSIN,SILENT HEMOLYSIN SHEA

 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  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL13Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:227 , LYS A:230 , HOH A:665 , HOH A:704 , TYR C:30 , ALA C:238binding site for residue GOL A 401
02AC2SOFTWAREGLU A:46 , TYR A:54 , HOH A:524 , HOH A:673binding site for residue GOL A 402
03AC3SOFTWARESER A:138 , GLN A:139 , ASN A:142 , ASN A:233 , ASP A:237 , GLU B:252 , LYS C:234binding site for residue GOL A 403
04AC4SOFTWARELYS A:147 , GLU B:246 , ALA B:249 , HOH B:558 , HOH B:560binding site for residue GOL B 401
05AC5SOFTWAREARG B:49 , PHE B:50 , TYR B:54 , PHE B:221 , HOH B:502binding site for residue GOL B 402
06AC6SOFTWARESER B:138 , GLN B:139 , ASN B:142 , ASN B:233 , ASP B:237 , HOH B:613 , ASN C:128 , HOH C:574 , HOH C:625binding site for residue GOL B 403
07AC7SOFTWAREARG C:49 , TYR C:54 , PHE C:221 , HOH C:501 , HOH C:551binding site for residue GOL C 401
08AC8SOFTWARELYS A:230 , GLN A:231 , TYR C:30 , GLN C:231 , ASP C:235 , HOH C:620binding site for residue GOL C 402
09AC9SOFTWAREASN B:128 , THR B:244 , SER C:138 , GLN C:139 , ASN C:142 , ASN C:233 , ASP C:237 , LYS C:240binding site for residue GOL C 403
10AD1SOFTWAREGLU C:106 , SER C:110 , LYS C:113 , ARG C:261 , PHE C:262 , TYR C:263 , HOH C:659binding site for residue GOL C 404
11AD2SOFTWAREALA A:187 , GLY A:188 , LYS C:118 , ASP C:122 , LYS C:126 , HOH C:507 , HOH C:614binding site for residue GOL C 405
12AD3SOFTWAREASN A:142 , GLY A:146 , HOH A:609 , LYS C:234 , ASP C:237 , HOH C:595 , HOH C:597 , HOH C:641 , HOH C:672binding site for residue GOL C 406
13AD4SOFTWAREGLU D:46 , TYR D:54 , PHE D:221 , HOH D:518 , HOH D:526 , HOH D:534binding site for residue GOL D 401
14AD5SOFTWAREGLU B:276 , SER D:55 , ASP D:158 , SER D:164 , TYR D:165 , HOH D:517binding site for residue ACT D 402

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:6 -B:264
2D:6 -D:264

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PHQ)

(-) 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
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee.hhh.eeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phq A   6 CDKTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVLVGDIKTLLMDSQDKYFEATQTVYEWAGVATQLLAAYILLFDEYNEKKASAQKDILIKVLDDGITKLNEAQKSLLVSSQSFNNASGKLLALDSQLTNDFSEKSSYFQSQVDKIRKEAYAGAAAGVVAGPFGLIISYSIAAGVVEGKLIPELKNKLKSVQNFFTTLSNTVKQANKDIDAAKLKLTTEIAAIGEIKTETETTRFYCDYDDLMLSLLKEAAKKMINTANEYQKRHGKKT 296
                                    15        25        35        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 


Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....ee.hhh.ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phq B   6 CDKTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVLVGDIKTLLMDSQDKYFEATQTVYEWAGVATQLLAAYILLFDEYNEKKASAQKDILIKVLDDGITKLNEAQKSLLVSSQSFNNASGKLLALDSQLTNDFSEKSSYFQSQVDKIRKEAGVVAGPFGLIIVVEGKLIPELKNKLKSVQNFFTTLSNTVKQANKDIDAAKLKLTTEIAAIGEIKTETETTRFYCDYDDLMLSLLKEAAKKMINTANEYQKRHGKKTL 297
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 ||    191  ||   208       218       228       238       248       258       268       278       288         
                                                                                                                                                                                                     177|       194|                                                                                               
                                                                                                                                                                                                      184        202                                                                                               


Chain C from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eee.hhh.eeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phq C   6 CDKTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVLVGDIKTLLMDSQDKYFEATQTVYEWAGVATQLLAAYILLFDEYNEKKASAQKDILIKVLDDGITKLNEAQKSLLVSSQSFNNASGKLLALDSQLTNDFSEKSSYFQSQVDKIRKEAYAGAAAGVVAGPFGLIISYSIAAGVVEGKLIPELKNKLKSVQNFFTTLSNTVKQANKDIDAAKLKLTTEIAAIGEIKTETETTRFYCDYDDLMLSLLKEAAKKMINTANEYQKRHGKKTLFEVPEV 303
                                    15        25        35        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        


Chain D from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eee.hhh.eeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phq D   6 CDKTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVLVGDIKTLLMDSQDKYFEATQTVYEWAGVATQLLAAYILLFDEYNEKKASAQKDILIKVLDDGITKLNEAQKSLLVSSQSFNNASGKLLALDSQLTNDFSEKSSYFQSQVDKIRKEAYAGAAAGVVAGPFGLIISYSIAAGVVEGKLIPELKNKLKSVQNFFTTLSNTVKQANKDIDAAKLKLTTEIAAIGEIKTETETTRFYCDYDDLMLSLLKEAAKKMINTANEYQKRHGKK 295
                                    15        25        35        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
   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  (0, 0)

(no "SCOP Domain" information available for 4PHQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HLYE_ECOLI | P77335: 1qoy 2wcd 4pho

(-) Related Entries Specified in the PDB File

4pho 4PHO CONTAINS THE SAME VARIANT OF CLYA WITH THE WILD TYPE N- TERMINUS STARTING AT THR2