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The Open Protein Structure Annotation Network
PDB Keyword
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3mst

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

    Title Crystal structure of a Putative nitrate transport protein (TVN0104) from THERMOPLASMA VOLCANIUM at 1.35 A resolution. To be published
    Site JCSG
    PDB Id 3mst Target Id 400673
    Molecular Characteristics
    Source Thermoplasma volcanium gss1
    Alias Ids TPS29772,NP_110623.1, 433326 Molecular Weight 25146.53 Da.
    Residues 225 Isoelectric Point 5.39
    Sequence mdvgmpfagpvsfpllvieeelpfrihnicsetgkfdvvldsitnmpkyglkifagvridmysilgdes sgriytlrkgtladfnarilayydkaqvinadgdtcikmanegysalvgneisigksfrnrmkelgldl pscamastrridevieayeqgidfiknnheraaeiiskksgyyseevmkkiigiyghevtkkraelvgs relysrvvpelndieiig
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.35 Rfree 0.155
    Matthews' coefficent 2.07 Rfactor 0.119
    Waters 278 Solvent Content 40.45

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3mst
    1. Hydrogen sulfide and hemeproteins: knowledge and mysteries
    R Pietri, E Romn-Morales - Antioxidants & Redox , 2011 - online.liebertpub.com
     

    Protein Summary

    Pfam update: I have built this as a small DUF but have been able to assign it to the Periplasmic binding protein clan:
    ID DUF3834
    AC PF12916
    DE Protein of unknown function (DUF3834)
    AU Coggill P
    SE JCSG_target_400673
    GA 20.80 20.80;
    TC 20.80 21.10;
    NC 20.50 20.30;
    BM hmmbuild -o /dev/null HMM SEED
    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq
    TP Family
    CL CL0177

    This family is likely to be related to solute-binding lipo-proteins.

    NP_110623.1 from Thermoplasma volcanium, solved by Se-MAD up to 1.35 A resolution, reveals an alpha/beta fold consisting of two globule domains. There is no Pfam hit found, however, it is structurally similar to the other JCSG target, 3hn0 ( RMSD 3.6 for 219 aligned Ca, 11%id).

     

     

     

    FRmonomer.png

     

    The DALI hits are:

    DALI Summary
        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3hn0-A 17.2 3.6 219 280 11 PDB MOLECULE: NITRATE TRANSPORT PROTEIN; 2: 3hn0-B 16.5 3.6 221 280 11 PDB MOLECULE: NITRATE TRANSPORT PROTEIN; 3: 3e4r-A 15.4 4.7 215 291 11 PDB MOLECULE: NITRATE TRANSPORT PROTEIN; 4: 2i4c-A 14.4 4.2 213 401 8 PDB MOLECULE: BICARBONATE TRANSPORTER; 5: 2i48-A 14.4 4.2 211 399 9 PDB MOLECULE: BICARBONATE TRANSPORTER; 6: 2i49-A 14.3 4.2 212 398 8 PDB MOLECULE: BICARBONATE TRANSPORTER; 7: 2i4b-A 14.2 4.3 211 401 9 PDB MOLECULE: BICARBONATE TRANSPORTER; 8: 2czl-A 14.2 4.6 216 270 14 PDB MOLECULE: HYPOTHETICAL PROTEIN TTHA1568; 9: 2dbp-A 14.1 4.6 218 270 14 PDB MOLECULE: TTHA1568; 10: 3a3u-A 14.1 4.6 218 270 14 PDB MOLECULE: MENAQUINONE BIOSYNTHETIC ENZYME; 11: 2nxo-C 13.7 3.6 208 269 14 PDB MOLECULE: HYPOTHETICAL PROTEIN SCO4506; 12: 2nxo-B 13.5 3.9 208 266 14 PDB MOLECULE: HYPOTHETICAL PROTEIN SCO4506; 13: 2nxo-A 13.4 3.6 205 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN SCO4506; 14: 1zbm-A 13.3 4.7 209 264 16 PDB MOLECULE: HYPOTHETICAL PROTEIN AF1704; 15: 2g29-A 13.2 4.1 206 385 13 PDB MOLECULE: NITRATE TRANSPORT PROTEIN NRTA; 16: 2i6e-D 12.9 3.8 207 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 17: 2i6e-B 12.9 3.7 207 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 18: 2i6e-A 12.8 3.9 207 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 19: 2i6e-E 12.8 3.8 207 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 20: 2i6e-C 12.8 3.7 207 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 21: 2i6e-G 12.8 3.7 207 272 13 PDB MOLECULE: HYPOTHETICAL PROTEIN; 22: 2i6e-H 12.8 3.8 206 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 23: 2i6e-F 12.8 3.7 208 272 15 PDB MOLECULE: HYPOTHETICAL PROTEIN; 24: 2nxo-D 11.6 4.4 188 236 16 PDB MOLECULE: HYPOTHETICAL PROTEIN SCO4506; 25: 2de3-B 10.0 4.4 208 347 4 PDB MOLECULE: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B; 26: 2qpq-C 9.9 3.9 188 296 9 PDB MOLECULE: PROTEIN BUG27; 27: 2de4-B 9.8 4.3 213 347 5 PDB MOLECULE: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B; 28: 2de4-A 9.7 4.3 211 344 5 PDB MOLECULE: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B; 29: 2qpq-A 9.6 4.1 189 296 10 PDB MOLECULE: PROTEIN BUG27; 30: 2de3-A 9.4 4.3 207 344 5 PDB MOLECULE: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B; 31: 2qpq-B 9.4 3.9 184 291 10 PDB MOLECULE: PROTEIN BUG27; 32: 2de2-A 9.2 4.5 208 347 6 PDB MOLECULE: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B; 33: 1p99-A 8.9 4.7 170 255 9 PDB MOLECULE: HYPOTHETICAL PROTEIN PG110; 34: 2dvz-A 8.4 4.8 185 300 6 PDB MOLECULE: PUTATIVE EXPORTED PROTEIN; 35: 1xs5-A 7.7 4.6 160 240 13 PDB MOLECULE: MEMBRANE LIPOPROTEIN TPN32; 36: 3ir1-A 7.7 4.3 157 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 37: 3gxa-B 7.7 4.4 157 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 38: 3gxa-A 7.7 4.3 159 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 39: 2f5x-B 7.6 4.9 175 300 9 PDB MOLECULE: BUGD; 40: 3ir1-B 7.6 4.3 157 245 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 41: 3ir1-F 7.6 4.4 160 245 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 42: 3gxa-F 7.6 4.3 156 245 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 43: 3gxa-D 7.6 4.4 157 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 44: 3gxa-C 7.6 4.4 157 245 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 45: 3ir1-D 7.6 4.4 157 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 46: 3ir1-E 7.6 4.4 157 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 47: 3ir1-C 7.6 4.5 160 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 48: 3gxa-E 7.6 4.5 159 240 9 PDB MOLECULE: OUTER MEMBRANE LIPOPROTEIN GNA1946; 49: 2f5x-C 7.3 5.0 176 299 9 PDB MOLECULE: BUGD; 50: 2f5x-A 7.3 5.1 175 299 10 PDB MOLECULE: BUGD; 51: 2ozz-B 7.3 4.0 155 212 8 PDB MOLECULE: HYPOTHETICAL PROTEIN YHFZ; 52: 2ozz-A 7.2 4.3 160 230 8 PDB MOLECULE: HYPOTHETICAL PROTEIN YHFZ; 53: 3gzg-A 6.9 4.5 156 232 9 PDB MOLECULE: MOLYBDATE-BINDING PERIPLASMIC PROTEIN; PERMEASE; 54: 2h5y-B 6.9 4.6 158 233 9 PDB MOLECULE: MOLYBDATE-BINDING PERIPLASMIC PROTEIN; 55: 3gzg-C 6.9 4.5 156 232 9 PDB MOLECULE: MOLYBDATE-BINDING PERIPLASMIC PROTEIN; PERMEASE; 56: 2h99-A 6.8 4.6 149 215 12 PDB MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM; 57: 2h5y-A 6.8 4.5 156 232 9 PDB MOLECULE: MOLYBDATE-BINDING PERIPLASMIC PROTEIN; 58: 3gzg-B 6.8 4.6 156 232 9 PDB MOLECULE: MOLYBDATE-BINDING PERIPLASMIC PROTEIN; PERMEASE; 59: 2h5y-C 6.8 4.4 156 232 9 PDB MOLECULE: MOLYBDATE-BINDING PERIPLASMIC PROTEIN; 60: 2h9b-A 6.7 4.5 150 216 11 PDB MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM; 61: 2h98-B 6.7 4.3 153 216 8 PDB MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR CATM; 62: 2h99-B 6.7 4.4 150 217 9 PDB MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM; 63: 3cvg-D 6.6 4.1 162 268 11 PDB MOLECULE: PUTATIVE METAL BINDING PROTEIN; 64: 1amf-A 6.6 4.4 152 231 7 PDB MOLECULE: MOLYBDATE TRANSPORT PROTEIN MODA; 65: 1wod-A 6.6 4.6 151 231 7 PDB MOLECULE: MODA; 66: 1cb6-A 6.5 5.5 175 691 8 PDB MOLECULE: PROTEIN (LACTOFERRIN); 67: 3cr9-A 6.5 5.6 178 689 10 PDB MOLECULE: LACTOTRANSFERRIN; 68: 2iq8-A 6.5 4.6 111 264 9 PDB MOLECULE: PUTATIVE PREPHENATE DEHYDRATASE; 69: 3kn3-B 6.4 3.9 148 238 11 PDB MOLECULE: PUTATIVE PERIPLASMIC PROTEIN; 70: 1b1x-A 6.4 5.5 177 689 10 PDB MOLECULE: LACTOFERRIN;

     

    The superposition of  NP_110623.1 with DALI top hit (3hn0) shows that two structures adopt a very similar folds.

    FRsuper_3hn0.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    236.33 kB23:40, 18 Mar 2010gyewonActions
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