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(-) Description

Title :  SDIA IN COMPLEX WITH 3-OXO-C6-HOMOSERINE LACTONE
 
Authors :  N. X. Nguyen, Y. Nguyen, V. Sperandio, Y. Jiang
Date :  06 Feb 15  (Deposition) - 08 Apr 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Quorum Sensor, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nguyen, N. X. Nguyen, J. L. Rogers, J. Liao, J. B. Macmillan, Y. Jiang V. Sperandio
Structural And Mechanistic Roles Of Novel Chemical Ligands On The Sdia Quorum-Sensing Transcription Regulator.
Mbio V. 6 2015
PubMed-ID: 25827420  |  Reference-DOI: 10.1128/MBIO.02429-14

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR OF FTSQAZ GENE CLUSTER
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: SDIA, ECS2654, Z3004
    Organism Scientific: ESCHERICHIA COLI O157:H7
    Organism Taxid: 83334

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
14823Ligand/Ion3-OXO-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
14822Ligand/Ion3-OXO-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
14822Ligand/Ion3-OXO-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:101 , ARG A:116 , ARG A:117binding site for residue SO4 A 301
2AC2SOFTWARESER A:43 , TYR A:63 , TRP A:67 , TYR A:71 , ASP A:80 , TRP A:95 , SER A:134binding site for residue 482 A 302
3AC3SOFTWAREARG B:111 , ARG B:117 , ALA B:140binding site for residue SO4 B 301
4AC4SOFTWARESER B:43 , TYR B:63 , TRP B:67 , TYR B:71 , ASP B:80 , VAL B:82 , TRP B:95 , LEU B:106 , SER B:134binding site for residue 482 B 302
5AC5SOFTWARESER C:43 , CYS C:45 , PHE C:59 , TYR C:63 , TRP C:67 , TYR C:71 , ASP C:80 , LEU C:83 , TRP C:95 , HOH C:401binding site for residue 482 C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y15)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:50 -Pro A:51
2Ala A:140 -Arg A:141
3Val B:50 -Pro B:51
4Val C:50 -Pro C:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y15)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y15)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeee.........eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhh.hhhhhhhhhhh...eeeeeeee.....eeeeeeee........hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y15 A   5 DFFSWRRTMLLRFQRMETAEEVYHEIELQAQQLEYDYYSLCVRHPVPFTRPKVAFYTNYPEAWVSYYQAKNFLAIDPVLNPENFSQGHLMWNDDLFNEAQPLWEAARAHGLRRGVTQYLMLPNRALGFLSFSRCSAREIPILSDELQLKMQLLVRESLMALMRLNDEIVMTPEMNFSKREKEILRWTAEGKTSAEIAMILSISENTVNFHQKNMQKKINAPNKTQVACYAAATGLIHH 242
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeee.........eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhh.hhhhhhhhhhh...eeeeeeee.....eeeeeeee........hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y15 B   5 DFFSWRRTMLLRFQRMETAEEVYHEIELQAQQLEYDYYSLCVRHPVPFTRPKVAFYTNYPEAWVSYYQAKNFLAIDPVLNPENFSQGHLMWNDDLFNEAQPLWEAARAHGLRRGVTQYLMLPNRALGFLSFSRCSAREIPILSDELQLKMQLLVRESLMALMRLNDEIVMTPEMNFSKREKEILRWTAEGKTSAEIAMILSISENTVNFHQKNMQKKINAPNKTQVACYAAATGLIH 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       


Chain C from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeee.........eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhh.hhhhhhhhhhhh..eeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y15 C   2 QDTDFFSWRRTMLLRFQRMETAEEVYHEIELQAQQLEYDYYSLCVRHPVPFTRPKVAFYTNYPEAWVSYYQAKNFLAIDPVLNPENFSQGHLMWNDDLFNEAQPLWEAARAHGLRRGVTQYLMLPNRALGFLSFSRCSAREIPILSDELQLKMQLLVRESLMALMRLNDEIVMTPEMNFSKREKEILRWTAEGKTSAEIAMILSISENTVNFHQKNMQKKINAPNKTQVACYAAATGLIH 241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 4Y15)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y15)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q8XBD0_ECO57 | Q8XBD0: 4y13 4y17

(-) Related Entries Specified in the PDB File

4y13 4Y13 CONTAINS THE SAME PROTEIN IN COMPLEX WITH OCTANOYL-RAC-GLYCEROL
4y17