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The Open Protein Structure Annotation Network
PDB Keyword
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3mdq

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

    Title Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3mdq Target Id 397998
    Molecular Characteristics
    Source Cytophaga hutchinsonii atcc 33406
    Alias Ids TPS29624,YP_676947.1, _0023.001152_, _0066.001282_, 452674 Molecular Weight 35107.82 Da.
    Residues 314 Isoelectric Point 6.14
    Sequence msqrigvidmgtntfhllitdivndrphtlvneksavglgkggitkgfiteeamdraldtlkkfrvild ehavvhviatgtsavrsgsnkqvlidrikkevnidvevidgareaelifrgvqqavpmedhislamdig ggsvefiignkneilwkqsfeiggqrlidrfhvhdpmreddrvmmhnyfdevlvplekaintwrptqli gcsgtfdtlaemniqhhrekialekqtsyllslpdfnrlrkqlvastrrerlaiagmielradmvvvai cliehvlklvstnaitvstyslkegvlytmldgvkvgs
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.178
    Matthews' coefficent 2.49 Rfactor 0.153
    Waters 356 Solvent Content 50.66

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3mdq
    1. Enzymatic activity of the soybean ecto-apyrase GS52 is essential for stimulation of nodulation
    K Tanaka, CT Nguyen, M Libault, J Cheng - Plant , 2011 - Am Soc Plant Biol
     

    Protein Summary

    The CHU_0316 gene from Cytophaga hutchinsonii atcc 33406 encodes the YP_676947 protein that belongs to the Ppx-phosphatase family (PF02541). YP_676947 is a putative exopolyphosphatase (Ppx) containing two domains. There are several Ppx structures available (2flo, 1u6z,1t6d/1t6c,3cer, 2j4r) containing three domains, but YP_676947 lacks the third domain. It is known that Ppx functions as a dimer, however, the oligomeric state of 3mdq is a monomer.

    MI_single.png

    Figure 1.  3mdq structure in asu.

     

    Summary of a Dali structural similarity search using 3mdq as query:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3cer-C 37.2 2.1 299 333 26 PDB MOLECULE: POSSIBLE EXOPOLYPHOSPHATASE-LIKE PROTEIN; 2: 3cer-A 36.9 2.2 300 330 26 PDB MOLECULE: POSSIBLE EXOPOLYPHOSPHATASE-LIKE PROTEIN; 3: 3cer-D 36.7 2.2 299 330 26 PDB MOLECULE: POSSIBLE EXOPOLYPHOSPHATASE-LIKE PROTEIN; 4: 3cer-E 36.2 2.1 296 322 26 PDB MOLECULE: POSSIBLE EXOPOLYPHOSPHATASE-LIKE PROTEIN; 5: 3cer-B 34.7 2.2 298 330 26 PDB MOLECULE: POSSIBLE EXOPOLYPHOSPHATASE-LIKE PROTEIN; 6: 1u6z-A 34.5 2.6 297 498 24 PDB MOLECULE: EXOPOLYPHOSPHATASE; 7: 2flo-B 34.2 2.5 296 495 25 PDB MOLECULE: EXOPOLYPHOSPHATASE; 8: 1u6z-B 34.1 2.6 296 500 24 PDB MOLECULE: EXOPOLYPHOSPHATASE; 9: 2flo-C 34.1 2.5 297 496 25 PDB MOLECULE: EXOPOLYPHOSPHATASE; 10: 2flo-D 33.9 2.5 297 496 25 PDB MOLECULE: EXOPOLYPHOSPHATASE; 11: 2flo-A 33.9 2.6 297 496 25 PDB MOLECULE: EXOPOLYPHOSPHATASE; 12: 1t6d-A 31.4 3.0 295 303 23 PDB MOLECULE: EXOPOLYPHOSPHATASE; 13: 1t6c-A 31.3 3.2 296 306 23 PDB MOLECULE: EXOPOLYPHOSPHATASE; 14: 3hi0-B 31.3 2.2 280 493 24 PDB MOLECULE: PUTATIVE EXOPOLYPHOSPHATASE; 15: 2j4r-B 31.3 3.3 292 299 24 PDB MOLECULE: EXOPOLYPHOSPHATASE; 16: 2j4r-A 29.9 3.4 292 299 24 PDB MOLECULE: EXOPOLYPHOSPHATASE; 17: 3hi0-A 29.6 2.2 282 501 23 PDB MOLECULE: PUTATIVE EXOPOLYPHOSPHATASE; 18: 1t6d-B 28.3 4.0 295 300 23 PDB MOLECULE: EXOPOLYPHOSPHATASE; 19: 3cj1-A 19.9 3.5 272 419 12 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2; 20: 3cj7-A 19.8 3.5 271 419 12 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2; 21: 3cj9-A 19.8 3.5 271 419 12 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2; 22: 3cja-A 19.6 3.5 271 419 12 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2; 23: 3aap-A 19.0 4.1 266 353 13 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I; 24: 3aaq-A 18.9 3.7 261 349 13 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I; 25: 3aar-A 18.9 4.0 266 352 13 PDB MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I; 26: 1e4f-T 14.2 4.8 223 378 13 PDB MOLECULE: CELL DIVISION PROTEIN FTSA; 27: 1e4g-T 13.0 4.4 219 380 11 PDB MOLECULE: CELL DIVISION PROTEIN FTSA; 28: 3d2f-A 12.2 4.4 231 629 14 PDB MOLECULE: HEAT SHOCK PROTEIN HOMOLOG SSE1; 29: 3c7n-A 12.2 4.4 229 648 13 PDB MOLECULE: HEAT SHOCK PROTEIN HOMOLOG SSE1; 30: 3d2e-A 12.1 4.3 229 629 14 PDB MOLECULE: HEAT SHOCK PROTEIN HOMOLOG SSE1;


    The superposition between 3mdq and 3cer (Northeast Structural Genomics Consortium target) is shown below. 3cer also contains only two domains and misses the third domain at the C-terminus.

    super_3cer.png

    Figure 2. Superposition of 3mdq (green) with 3cer (cyan).

    Ligand Summary

    Reviews

    References

     

    No references found.

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    204.18 kB00:28, 24 Mar 2010gyewonActions
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