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(-) Description

Title :  CRYSTAL STRUCTURE OF E. FAECALIS DNA BINDING DOMAIN LIARD191N COMPLEXED WITH 26BP DNA
 
Authors :  M. Davlieva, Y. Shamoo
Date :  02 Nov 14  (Deposition) - 06 May 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,H
Keywords :  Helix-Turn-Helix, Response Regulator, Enterococci, Dna Binding Domain, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Davlieva, Y. Shi, P. G. Leonard, T. A. Johnson, M. R. Zianni, C. A. Arias, J. E. Ladbury, Y. Shamoo
A Variable Dna Recognition Site Organization Establishes Th Liar-Mediated Cell Envelope Stress Response Of Enterococci To Daptomycin.
Nucleic Acids Res. V. 43 4758 2015
PubMed-ID: 25897118  |  Reference-DOI: 10.1093/NAR/GKV321

(-) Compounds

Molecule 1 - RESPONSE REGULATOR RECEIVER DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
 
Molecule 2 - DNA (26-MER)
    Chains: H
    Engineered: YES
    Organism Scientific: ENTEROCOCCUS FAECALIS S613
    Organism Taxid: 699185
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: ENTEROCOCCUS FAECALIS S613
    Organism Taxid: 699185
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4WUL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His B:142 -Glu B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WUL)

(-) 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:65
                                                                                                  
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                4wul A  141 LHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDNRTQAAIYAFQHGLA  205
                                   150       160       170       180       190       200     


Chain B from PDB  Type:PROTEIN  Length:64
                                                                                                 
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                4wul B  142 HEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDNRTQAAIYAFQHGLA  205
                                   151       161       171       181       191       201    


Chain C from PDB  Type:DNA  Length:26
                                                           
                4wul C  -99 ATTTCTTCTCATTAGTAAGGACTAGT -124
                            ||||||-108||||||-118||||||
                          -99|||||-108|||||-117|||||||
                          -100|||||-109|||||-118||||||
                           -101|||||-110|||||-119|||||
                            -102|||||-111|||||-120||||
                             -103|||| -112|||| -121|||
                              -104|||  -113|||  -122||
                               -105||   -114||   -123|
                                -106|    -115|    -124
                                 -107     -116        


Chain H from PDB  Type:DNA  Length:26
                                                           
                4wul H -124 ACTAGTCCTTACTAATGAGAAGAAAT  -99
                                  -115      -105
   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 4WUL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His B:142 - Glu B:143   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        D4EMQ0_ENTFL | D4EMQ0: 4wsz 4wt0 4wu4 4wuh

(-) Related Entries Specified in the PDB File

4wsz 4wt0 4wu4 4wuh