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The Open Protein Structure Annotation Network
PDB Keyword
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3jx9

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

    Title Crystal structure of Putative phosphoheptose isomerase (YP_001815198.1) from EXIGUOBACTERIUM SP. 255-15 at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 3jx9 Target Id 392463
    Molecular Characteristics
    Source Exiguobacterium sibiricum 255-15
    Alias Ids TPS26559,YP_001815198.1, 325578 Molecular Weight 18981.79 Da.
    Residues 169 Isoelectric Point 5.10
    Sequence mlkilatqfngklqtltkqedelfdvvrllaqalvgqgkvyldaygefeglypmlsdgpdqmkrvtkik dhktlhavdrvliftpdtersdllaslarydawhtpysiitlgdvtetlersiaplalkfdkgllpaed gsrhglpslalgafllthiltqlqemteewe
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.95 Rfree 0.188
    Matthews' coefficent 2.94 Rfactor 0.163
    Waters 312 Solvent Content 58.18

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3jx9

    Protein Summary

    Pfam update:This sequence is now obsolete. I dont understand this comment - this protein shows up both in NCBI (http://www.ncbi.nlm.nih.gov/protein/YP_001815198.1) and UniProt (http://www.uniprot.org/uniprot/B1YEL3). In the other hand, its is not included in NCBI NR database.

    Gene Exig_2733 from Exiguobacterium sp. 255-15 encodes the YP_001815198.1 protein with 169 residues belonging to Pfam DUF2529 family ( PF10740). It is present as a dimer in the crystal structure and crystal packing analysis suggests that this dimer should be the stable oligomeric form in solution.

    dimer_123222.png

    DALI suggests that the structure is similar to phosphoheptose isomerase. The superposition of 3jx9 (light green) with (putative) phosphoheptose isomerases - 3cvj (light blue) and 3bjz (light pink) - are shown below.
     sup_gr123222_bl3cvj_pi3bjz_.png

    The biological unit of 3jx9 and 1cvj is a dimer; in contrast, the biological unit of 3bjz is a tetramer.

    DALI Summary

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3cvj-B 16.9 2.2 168 243 14 PDB MOLECULE: PUTATIVE PHOSPHOHEPTOSE ISOMERASE; 2: 3cvj-D 16.9 2.2 168 242 15 PDB MOLECULE: PUTATIVE PHOSPHOHEPTOSE ISOMERASE; 3: 3cvj-C 16.8 2.2 166 242 14 PDB MOLECULE: PUTATIVE PHOSPHOHEPTOSE ISOMERASE; 4: 3bjz-A 16.8 2.1 153 179 8 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 5: 3cvj-A 16.7 2.2 166 243 14 PDB MOLECULE: PUTATIVE PHOSPHOHEPTOSE ISOMERASE; 6: 3bjz-C 16.6 2.1 153 179 8 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 7: 3bjz-D 16.5 2.2 153 176 8 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 8: 2i22-D 16.4 2.3 153 178 10 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 9: 2i2w-B 16.4 2.3 154 177 10 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 10: 3bjz-B 16.4 2.2 153 186 8 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 11: 2i22-C 16.3 2.3 153 178 10 PDB MOLECULE: PHOSPHOHEPTOSE ISOMERASE; 12: 1x94-B 16.3 2.3 153 176 10 PDB MOLECULE: PUTATIVE PHOSPHOHEPTOSE ISOMERASE; 13: 3etn-A 16.3 2.7 161 192 12 PDB MOLECULE: PUTATIVE PHOSPHOSUGAR ISOMERASE INVOLVED IN 14: 3etn-C 16.3 2.7 161 192 12 PDB MOLECULE: PUTATIVE PHOSPHOSUGAR ISOMERASE INVOLVED IN 15: 2yva-A 16.2 2.2 153 193 10 PDB MOLECULE: DNAA INITIATOR-ASSOCIATING PROTEIN DIAA;

    Ligand Summary


     

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