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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF AGRA LYTTR DOMAIN IN COMPLEX WITH PROMOTERS
 
Authors :  B. Gopal, K. Rajasree
Date :  19 Jan 15  (Deposition) - 27 Apr 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dna Complex, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gopal, K. Rajasree
Conformational Features Of The Staphylococcus Aureus Agra-Promoter Interactions Rationalize Quorum-Sensing Triggered Gene Expression
Biochem Biophys Rep 2016
PubMed: search  |  Reference-DOI: 10.1016/J.BBREP.2016.03.012

(-) Compounds

Molecule 1 - ACCESSORY GENE REGULATOR A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LYTTR DOMAIN (UNP RESIDUES 139-238)
    Gene: AGRA, SACOL2026
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN COL)
    Organism Taxid: 93062
    Strain: COL
 
Molecule 2 - DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)- 3')
    Chains: E, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)- 3')
    Chains: F, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 4XQQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XQQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhhhh..eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4xqq A 140 VETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   149       159       169       179       189       199       209       219       229         


Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhhhh..eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4xqq B 141 ETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   150       160       170       180       190       200       210       220       230        


Chain C from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhhhh..eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4xqq C 140 VETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   149       159       169       179       189       199       209       219       229         


Chain D from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhhhh..eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4xqq D 139 SVETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   148       158       168       178       188       198       208       218       228       238


Chain E from PDB  Type:DNA  Length:16
                                                
                 4xqq E   1 TCGACTAGTTAAGAAA  16
                                    10      


Chain F from PDB  Type:DNA  Length:16
                                                
                 4xqq F   1 ATTTCTTAACTAGTCG  16
                                    10      


Chain G from PDB  Type:DNA  Length:16
                                                
                 4xqq G   1 TCGACTAGTTAAGAAA  16
                                    10      


Chain H from PDB  Type:DNA  Length:16
                                                
                 4xqq H   1 ATTTCTTAACTAGTCG  16
                                    10
   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 4XQQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Cis Peptide Bonds" information available for 4xqq)
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        AGRA_STAAC | Q5HEG2: 4xqj 4xqn 4xxe 4xyo 4xyq

(-) Related Entries Specified in the PDB File

4xqj 4xqn