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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) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
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, 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 140-238)
    Gene: AGRA, SACOL2026
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN COL)
    Organism Taxid: 93062
    Strain: COL
 
Molecule 2 - DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3EOH14Ligand/IonETHANOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3EOH8Ligand/IonETHANOL
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3EOH6Ligand/IonETHANOL

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:147 , GLN A:179 , ILE A:180 , GLU A:181 , EOH A:302 , ASN D:177 , ARG D:178 , GLN D:179binding site for residue EOH A 301
02AC2SOFTWAREARG A:147 , EOH A:301binding site for residue EOH A 302
03AC3SOFTWAREGLU A:144 , LYS A:146 , PHE A:182 , TYR A:183binding site for residue EOH A 303
04AC4SOFTWAREARG A:147 , ARG A:170 , GLU A:181 , EOH A:305binding site for residue EOH A 304
05AC5SOFTWAREARG A:147 , SER A:149 , ASN A:150 , EOH A:304 , DA C:1 , DA C:2 , ASN D:177binding site for residue EOH A 305
06AC6SOFTWAREASN A:201 , ASN A:234 , DC C:10binding site for residue EOH A 306
07AC7SOFTWAREPHE A:161 , GLU A:163 , HIS A:227 , HOH A:437binding site for residue EOH A 307
08AC8SOFTWAREVAL A:140 , HOH A:418 , HOH A:430binding site for residue EDO A 309
09AC9SOFTWARESER A:151 , VAL A:152 , TYR A:153 , ASP A:158 , HOH A:401 , HOH A:402binding site for residue EDO A 310
10AD1SOFTWAREARG A:195 , ARG A:207 , HIS A:208 , DT B:16binding site for residue EOH B 101
11AD2SOFTWAREDA C:8 , HOH C:211binding site for residue EDO C 101
12AD3SOFTWAREARG D:147 , ARG D:170 , GLU D:181 , HOH D:446binding site for residue EOH D 301
13AD4SOFTWARESER D:149 , VAL D:152 , TYR D:153 , ARG D:178binding site for residue EOH D 302
14AD5SOFTWAREASN D:201 , HOH E:207 , HOH E:214 , DA F:9 , HOH F:202 , HOH F:203binding site for residue EOH D 303
15AD6SOFTWARESER D:165 , LYS D:167 , HIS D:169 , ARG D:170 , HOH D:409 , HOH D:432 , DA E:11 , DA E:12binding site for residue EDO D 304
16AD7SOFTWAREHOH A:405 , HOH A:409 , HOH A:421 , HOH E:205 , HOH E:206 , HOH E:208 , HOH F:202 , HOH F:204binding site for residue CA E 101
17AD8SOFTWAREASP D:194 , ARG D:195 , ARG D:207 , HIS D:208 , DT E:16binding site for residue EOH E 102
18AD9SOFTWAREDG E:8 , DT E:9 , DT F:11binding site for residue EDO E 103
19AE1SOFTWAREASP A:193 , HOH A:413 , HOH A:416 , HOH A:418 , DA F:9 , HOH F:206binding site for residue CA F 101
20AE2SOFTWARESER D:212 , DT F:4 , DC F:5binding site for residue EOH F 102
21AE3SOFTWARELEU A:192 , DA F:8binding site for residue EOH F 103
22AE4SOFTWAREILE D:210 , EDO F:105binding site for residue EDO F 104
23AE5SOFTWAREDT F:4 , DC F:5 , EDO F:104 , HOH F:215binding site for residue EDO F 105
24AE6SOFTWAREHIS D:200 , ASN D:201 , ASN D:234 , DC F:10 , DT F:11binding site for residue EDO F 106

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XQJ)

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


Chain B from PDB  Type:DNA  Length:12
                                            
                 4xqj B   5 ACAGTTAAGAAT  16
                                    14  


Chain C from PDB  Type:DNA  Length:13
                                             
                 4xqj C   1 AATTCTTAACTGT  13
                                    10   


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeee...eeeeee.....eeeeee...eeeee.hhhhhhh....eeeee..eeee...eeeee....eeee....eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4xqj D 140 VETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKK 237
                                   149       159       169       179       189       199       209       219       229        


Chain E from PDB  Type:DNA  Length:11
                                           
                 4xqj E   6 CAGTTAAGAAT  16
                                    15 


Chain F from PDB  Type:DNA  Length:13
                                             
                 4xqj F   1 AATTCTTAACTGT  13
                                    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 4XQJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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(-) Related Entries Specified in the PDB File

4xqn 4xqq