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The Open Protein Structure Annotation Network
PDB Keyword
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3k69

    Table of contents
        1. 1.1.1. Protein Summary
    1. 2.  
        1. 2.1.1. Ligand Summary

    Title Crystal structure of Putative transcriptional regulator (NP_784167.1) from LACTOBACILLUS PLANTARUM at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 3k69 Target Id 396747
    Molecular Characteristics
    Source Lactobacillus plantarum wcfs1
    Alias Ids TPS27998,NP_784167.1, 327014 Molecular Weight 17893.06 Da.
    Residues 161 Isoelectric Point 5.44
    Sequence mggsnmkldfsvavhsilyldahrdskvasrelaqslhlnpvmirnilsvlhkhgyltgtvgknggyql dlaladmnlgdlydltipptisyarfitgpsktdeqadqspiaanisetltdlftvadrqyrayyhqft madlqadlnhhgtflqheqdses
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.95 Rfree 0.218
    Matthews' coefficent 2.36 Rfactor 0.172
    Waters 161 Solvent Content 47.86

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3k69
    1. Insights into the Rrf2 repressor familythe structure of CymR, the global cysteine regulator of Bacillus subtilis
    W Shepard, O Soutourina, E Courtois, P England - FEBS , 2011 - Wiley Online Library
     

    Protein Summary

    Gene lp_0360 from Lactobacillus plantarum encodes the NP_784167.1 protein which belongs to the Rrf2 group ( PF02082 ). Pre-SCOP classifies 3k69 in the all alpha class, winged helix DNA binding domain superfamily, transcriptional regulator Rrf2 family. Although the protein structure of 3k69 is a monomer in the asu, the likely biological molecule is a dimer.

     monomer_127124.png

    Fig 1. Monomer of 3k69 found in the asu.

     

     

    dimer_127124.png

    Fig 2. Biological dimer of 3k69

     

    super_1ylf.png

     

     

     

     

     

    Fig 2. Superposition of 3k69 with DALI top hit (1ylf).

     

    Dali search of 3k69 hits with many transcriptional regulator proteins as shown below.

     

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
       1:  1ylf-C 14.4  2.3  119   119   30 PDB  MOLECULE: RRF2 FAMILY PROTEIN;                                       
       2:  1ylf-B 14.0  1.7  117   118   32 PDB  MOLECULE: RRF2 FAMILY PROTEIN;                                       
       3:  1ylf-A 13.3  1.9  115   117   31 PDB  MOLECULE: RRF2 FAMILY PROTEIN;                                       
       4:  1xd7-A 12.2  2.1  116   116   25 PDB  MOLECULE: YWNA;                                                      
       5:  3cuo-A  7.8  2.0   73    98   14 PDB  MOLECULE: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL                   
       6:  3cuo-C  7.8  2.0   72    95   14 PDB  MOLECULE: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL                   
       7:  3cuo-B  7.7  2.0   73    98   14 PDB  MOLECULE: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL                   
       8:  1qbj-A  7.5  1.6   64    65   16 PDB  MOLECULE: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE            
       9:  3f23-A  7.5  1.6   64    65   16 PDB  MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC ADENOSINE DEAMINASE;          
      10:  1r23-A  7.4  2.5   74   104   14 PDB  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;                            
      11:  3f22-A  7.4  1.6   64    65   16 PDB  MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC ADENOSINE DEAMINASE;          
      12:  2rdp-A  7.3  3.6   81   140   10 PDB  MOLECULE: PUTATIVE TRANSCRIPTIONAL REGULATOR MARR;                   
      13:  3cuo-D  7.3  2.2   71    94   14 PDB  MOLECULE: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL                   
      14:  1r1t-B  7.3  2.3   71    99   15 PDB  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;                            
      15:  3f22-C  7.3  1.7   65    66   15 PDB  MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC ADENOSINE DEAMINASE;          
      16:  3f23-C  7.3  1.7   65    66   15 PDB  MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC ADENOSINE DEAMINASE;          
      17:  1r23-B  7.2  2.6   74    97   14 PDB  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;                            
      18:  1smt-A  7.2  2.6   74    98   14 PDB  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;                            
      19:  1smt-B  7.2  2.5   73   101   15 PDB  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;                            
      20:  1r1t-A  7.2  2.8   74    98   14 PDB  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;

    Ligand Summary

    -  DIMETHYL SULFOXIDE (DMS)
     

    Reviews

    References

     

    No references found.

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