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(-) Description

Title :  CRYSTAL STRUCTURE OF E. FAECALIS DNA BINDING DOMAIN LIARD191N COMPLEXED WITH 22BP DNA
 
Authors :  M. Davlieva, Y. Shamoo
Date :  31 Oct 14  (Deposition) - 06 May 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,G,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
 
Molecule 2 - DNA (5'- D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: ENTEROCOCCUS FAECALIS S613
    Organism Taxid: 699185
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')
    Chains: H
    Engineered: YES
    Organism Scientific: ENTEROCOCCUS FAECALIS S613
    Organism Taxid: 699185
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:158 , HOH A:422 , GLN B:194 , TYR B:198 , HOH B:304binding site for residue GOL A 301
2AC2SOFTWAREDT G:-91 , DA G:-92 , DG H:-89 , DA H:-90 , HOH H:208 , HOH H:215binding site for residue GOL H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WU4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WU4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WU4)

(-) Exons   (0, 0)

(no "Exon" information available for 4WU4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:68
                                                                                                     
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                4wu4 A  139 MVLHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDNRTQAAIYAFQHGLAK  206
                                   148       158       168       178       188       198        


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                     
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                4wu4 B  139 MVLHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDNRTQAAIYAFQHGLAK  206
                                   148       158       168       178       188       198        


Chain G from PDB  Type:DNA  Length:17
                                                  
                4wu4 G  -86 GGACTTAAGAACGATTT -102
                            |||||||-95|||||||
                          -86||||||-95|||||||
                           -87||||||-96||||||
                            -88||||||-97|||||
                             -89||||| -98||||
                              -90||||  -99|||
                               -91|||  -100||
                                -92||   -101|
                                 -93|    -102
                                  -94        


Chain H from PDB  Type:DNA  Length:17
                                                  
                4wu4 H -102 AAATCGTTCTTAAGTCC  -86
                                   -93
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  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 4WU4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WU4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WU4)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4wsz 4wu4 4wuh 4wul