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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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS27998,NP_784167.1, 327014
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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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