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(-) Description

Title :  CRYSTAL STRUCTURE OF E. FAECALIS DNA BINDING DOMAIN LIAR WILD TYPE 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 :  2.29
Chains :  Asym./Biol. Unit :  A,B,C,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
    Fragment: DNA BINDING DOMAIN
    Gene: HMPREF9376_01931
    Organism Scientific: ENTEROCOCCUS FAECALIS S613
    Organism Taxid: 699185
    Strain: S613
 
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*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
 
Molecule 4 - DNA (5'-D(P*AP*AP*AP*TP*CP*G)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: ENTEROCOCCUS FAECALIS S613
    Organism Taxid: 699185
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCGH

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
1AC1SOFTWAREASN B:148 , HIS B:151binding site for residue GOL B 301
2AC2SOFTWAREDA G:92 , HOH G:311 , HOH G:317 , DG H:-95 , DA H:-96binding site for residue GOL G 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WUH)

(-) 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    
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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
                4wuh A  140 MVLHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDNRTQAAIYAFQHGLAK  207
                                   149       159       169       179       189       199        


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
                4wuh B  140 MVLHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDNRTQAAIYAFQHGLAK  207
                                   149       159       169       179       189       199        


Chain C from PDB  Type:DNA  Length:6
                                       
                4wuh C    0 AAATCG    5


Chain G from PDB  Type:DNA  Length:17
                                                  
                4wuh G   86 GGACTTAAGAACGATTT  102
                                    95       


Chain H from PDB  Type:DNA  Length:11
                                            
                4wuh H -102 TTCTTAAGTCC  -92
                                   -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 4WUH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  4wuh
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4wsz 4wt0 4wu4 4wul