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The Open Protein Structure Annotation Network
PDB Keyword
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3kh1

    Title Crystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from Magnetospirillum magnetotacticum MS-1 at 1.37 A resolution ;. To be published
    Site JCSG
    PDB Id 3kh1 Target Id 394528
    Molecular Characteristics
    Source Magnetospirillum magneticum amb-1
    Alias Ids TPS25810,MMAG_12JAN01_CONTIG3870_REVISED_GENE3381, _0109.000515_ Molecular Weight 22467.14 Da.
    Residues 199 Isoelectric Point 5.22
    Sequence mipfpesrlaaqmsfvveidklktilrqtlltdssrrendaehswhiatmafllaeyadeavqigrvar mllihdiveidagdtfihdeagnedkeererkaaarlfgllppdqaaeysalwqeyearetadarfada ldrlqpllhnfeteggtwkphgvtrakvdkllprieagskrlgayaralvdeavrrgylap
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.37 Rfree 0.164
    Matthews' coefficent 2.29 Rfactor 0.132
    Waters 515 Solvent Content 46.24

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This protein ZP_00055740.2 is predicted to be a hydrolase of HD superfamily [Magnetospirillum magnetotacticum MS-1]. ZP_00055740.2 belongs to PFAM PF01966 HD which consists of HD domains which are metal dependent phosphohydrolases.

    The monomer structure is shown below.

    MH11587E.png

    The protein assembles as a dimer in the crystal structure and most likely represents its biological oligomeric state.

    MH11587E_dimer.png

     

    There are several structural homologs of this protein.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE (JCSG structures highlighted in red)
    1 2cqz 15.2 2.8 158 173 18 177AA LONG HYPOTHETICAL PROTEIN
    2 1xx7 14.5 2.8 153 172 25 OXETANOCIN-LIKE PROTEIN
    3 1wph 14.3 3.3 160 176 23 HYPOTHETICAL UPF0207 PROTEIN YFBR
    4 2paq 14.2 3.3 160 176 23 5'-DEOXYNUCLEOTIDASE YFBR
    5 2pau 14.0 3.2 158 177 21 5'-DEOXYNUCLEOTIDASE YFBR
    6 2par 14.0 3.5 161 178 22 5'-DEOXYNUCLEOTIDASE YFBR
    7 1ynb 12.2 3.2 146 167 19 HYPOTHETICAL PROTEIN AF1432
    8 1yoy 9.7 3.5 132 146 20 HYPOTHETICAL PROTEIN AF1432
    9 2pjq 8.6 3.5 141 212 12 UNCHARACTERIZED PROTEIN LP_2664
    10 1vj7 8.4 3.0 132 310 11 BIFUNCTIONAL RELA/SPOT

     

    A superposition of these proteins is shown below.

    MH11587E_all.png

    Color scheme: ZP_00055740.2 (green), 1vj7 (cyan), 1wph (lightmagenta), 1xx7 (yellow), 1ynb (salmon), 1yoy (lightgrey), 2cqz (slate), 2paq (orange), 2par (lime), 2pau (deepteal), 2pjq (hotpink).

    Ligand Summary

    Reviews

    References

     

    No references found.

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