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The Open Protein Structure Annotation Network
PDB Keyword
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3qc0

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

    Title Crystal structure of a sugar isomerase (SMc04130) from SINORHIZOBIUM MELILOTI 1021 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3qc0 Target Id 403584
    Molecular Characteristics
    Source Sinorhizobium meliloti 1021
    Alias Ids TPS30784,NP_384228.1, _0083.001658_, 332677 Molecular Weight 29305.11 Da.
    Residues 274 Isoelectric Point 5.67
    Sequence mqveglsinlatireqcgfaeavdiclkhgitaiapwrdqvaaiglgeagrivranglkltglcrggff papdasgrekaiddnrravdeaaelgadclvlvagglpggsknidaarrmvvegiaavlpharaagvpl aieplhpmyaadracvntlgqaldicetlgpgvgvaidvyhvwwdpdlanqiaragkmkailahhicdw lvptkdmltdrgmmgdgvidlkgirrrieaagfhgaqeveifsadnwwkrpadeviatcveryrncc
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.45 Rfree 0.1846
    Matthews' coefficent 3.22 Rfactor 0.1594
    Waters 275 Solvent Content 61.81

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam update:This protein matches the Pfam entry AP_endonuc_2 (PF01261). There are already several stucture for this family.

    Gene 1231753_SMc04130 from Sinorhizobium meliloti 1021 encodes the NP_384228.1 amino acid sequence of a putative uncharaterized protein belonging to the Pfam; PF01261; AP_endonuc_2 family.

    There is only one molecule found in the asu. However, PISA predicts a dimer as a biomolecule.

    monomer.png

    Fig 1. NP_384228.1 structure as seen in the asu.

    oligomer_dimer.png

    Fig 2. Biological dimer of NP_384228.1

     

    DALI hits are shown below.

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3ju2-A 49.5 0.3 273 275 98 PDB MOLECULE: UNCHARACTERIZED PROTEIN SMC04130; 2: 1i60-A 30.6 2.2 259 278 24 PDB MOLECULE: IOLI PROTEIN; 3: 1i6n-A 30.6 2.2 259 278 24 PDB MOLECULE: IOLI PROTEIN; 4: 2q02-B 27.8 2.3 250 272 15 PDB MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; 5: 2q02-A 27.7 2.3 249 272 15 PDB MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; 6: 2q02-C 27.7 2.3 249 271 15 PDB MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; 7: 2q02-D 27.7 2.3 249 272 15 PDB MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; 8: 2g0w-A 26.7 2.5 250 275 15 PDB MOLECULE: LMO2234 PROTEIN; 9: 2g0w-B 26.3 2.5 250 285 15 PDB MOLECULE: LMO2234 PROTEIN; 10: 2zvr-B 26.2 2.3 239 262 18 PDB MOLECULE: UNCHARACTERIZED PROTEIN TM_0416; 11: 3ktc-A 26.1 2.8 256 330 15 PDB MOLECULE: XYLOSE ISOMERASE; 12: 3ktc-B 26.0 2.8 257 330 15 PDB MOLECULE: XYLOSE ISOMERASE; 13: 2qul-D 26.0 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 14: 2qul-C 26.0 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 15: 2qul-A 26.0 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 16: 2qum-A 26.0 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 17: 2ou4-C 26.0 2.5 254 289 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 18: 2qun-D 26.0 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 19: 2ou4-A 25.9 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 20: 2qul-B 25.9 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 21: 2qum-D 25.9 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 22: 2qum-C 25.9 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 23: 2qum-B 25.9 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 24: 2ou4-B 25.9 2.5 254 289 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 25: 2zvr-A 25.9 2.3 239 259 18 PDB MOLECULE: UNCHARACTERIZED PROTEIN TM_0416; 26: 2qun-A 25.8 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 27: 2qun-B 25.8 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 28: 2qun-C 25.8 2.5 254 290 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 29: 2ou4-D 25.8 2.5 254 289 17 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 30: 1k77-A 25.3 2.6 245 260 20 PDB MOLECULE: HYPOTHETICAL PROTEIN YGBM; 31: 2hk0-A 25.3 2.6 252 289 19 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 32: 2hk0-D 25.3 2.6 252 289 19 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 33: 2hk1-D 25.2 2.5 251 289 20 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 34: 2hk1-A 25.2 2.6 251 289 20 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 35: 2hk1-C 25.2 2.6 252 289 19 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 36: 1o1h-A 25.2 2.8 264 386 20 PDB MOLECULE: XYLOSE ISOMERASE; 37: 1s5m-A 25.2 2.8 264 386 20 PDB MOLECULE: XYLOSE ISOMERASE; 38: 1o1h-B 25.2 2.8 265 386 20 PDB MOLECULE: XYLOSE ISOMERASE; 39: 2hk0-C 25.1 2.6 252 289 19 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 40: 2hk0-B 25.1 2.6 252 289 19 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 41: 1xlc-B 25.1 2.8 266 393 20 PDB MOLECULE: D-XYLOSE ISOMERASE; 42: 1s5n-A 25.1 2.8 264 386 20 PDB MOLECULE: XYLOSE ISOMERASE; 43: 2gyi-A 25.1 2.8 264 385 20 PDB MOLECULE: XYLOSE ISOMERASE; 44: 2glk-A 25.1 2.8 264 388 20 PDB MOLECULE: XYLOSE ISOMERASE; 45: 1muw-A 25.1 2.8 264 386 20 PDB MOLECULE: XYLOSE ISOMERASE; 46: 3kws-A 25.0 2.7 248 265 18 PDB MOLECULE: PUTATIVE SUGAR ISOMERASE; 47: 3gnx-E 25.0 2.8 264 385 20 PDB MOLECULE: XYLOSE ISOMERASE; 48: 2hk1-B 25.0 2.6 251 289 20 PDB MOLECULE: D-PSICOSE 3-EPIMERASE; 49: 3kws-B 25.0 2.7 248 265 18 PDB MOLECULE: PUTATIVE SUGAR ISOMERASE; 50: 1xlg-B 25.0 2.8 266 393 20 PDB MOLECULE: D-XYLOSE ISOMERASE;

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

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     monomer.png
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    233.03 kB00:30, 9 Apr 2010gyewonActions
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    283.06 kB00:30, 9 Apr 2010gyewonActions
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