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4mcj

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

    Title Crystal structure of a hypothetical protein (BDI_0649) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution. To be published
    Site JCSG
    PDB Id 4mcj Target Id 394800
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25374,YP_001302047.1, 533782 Molecular Weight 17781.53 Da.
    Residues 153 Isoelectric Point 5.23
    Sequence aqsevvvlypdtenkdldeavyqkiflagtidmgksvdwqkatcdwfralpegryllfnprrdkglsge msdfehqvnwelehlekadliimnilasskspitllemglfmrsgklrvicepgfyrydnvrltcaryg vplyqnmddflktmr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 10
    Resolution (Å) 2.40 Rfree 0.2125
    Matthews' coefficent 3.00 Rfactor 0.1850
    Waters 574 Solvent Content 59.00

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Update: It looks as if this is a subset of Nucleoside deoxyribosyltransferases from clan Nribosyltransf (CL0498). On building it there were some overlaps with the original Nuc-deoxyrib_tr family PF05014, which does have some structures. Looking at the sequnce motifs, there is a characteristic FLAG-like conserved motif at the N-terminus, also found in the other clan members, and several conserved Glutamines, which appear It will be very interesting to have the structure for comparison, and to determine if all the active sites are conserved and thus if the activity is similar or slightly different.

     

    Shown below is a ribbons representation of the structure color-coded with the N-terminal end in blue and the C-terminal end in red

    monomer.png

     


    The crystal structure indicates the dimer as a significant oligomerization state. Shown below is a ribbons representation of the dimer

     

    dimer.png

     

    A search of the SCOP database shows that the structure is a flavodoxin-like fold and a member of the N-deoxyribosyltransferase SCOP family. A DALI structural similarity search shows that target id is related in structure to the following targets,

     

    PDB ID DALI Z-score rmsd (Ang) length of alignment totalnumber of residues in related structure sequence id (%) Description
    3ehd 10.6 3.1 123 158 13 Crystal structure of conserved protein from Enterococcus faecalis V583 (MCSG
    2klh 10.5 2.9 120 156 13 NMR Structure of RCL in complex with GMP[Ref]
    2khz 10.2 2.8 120 163 11 Solution Structure of RCL[Ref]
    4fyk 10.0 2.6 108 126 12 Crystal structure of rcl with 5'-phiosphorothioate-adenosine [Ref]
    4fyi 9.9 2.6 108 126 12 Crystal structure of rcl with 6-cyclopentyl-AMP[Ref]
    1s3f 9.8 3.0 117 165 9 Purine 2'-deoxyribosyltransferase + selenoinosine [Ref]  
    1s2g 9.8 3.3 118 167 9 Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine [Ref]
    1s2i 9.8 3.1 117 165 9 Purine 2'deoxyribosyltransferase + bromopurine[Ref]
    1s2l 9.8 2.8 112 153 8 Purine 2'deoxyribosyltransferase native structure[Ref]

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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    115.63 kB17:41, 23 May 2013haxelrodActions
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    91.26 kB17:41, 23 May 2013haxelrodActions
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