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The Open Protein Structure Annotation Network
PDB Keyword
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1vmh

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

    Title Crystal structure of Uncharacterized conserved protein YjbQ/UPF0047 family, ortholog yugU B.subtilis (15023806) from Clostridium acetobutylicum at 1.31 A resolution. To be published
    Site JCSG
    PDB Id 1vmh Target Id 357074
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS1373,15023806, 289433, 289424 Molecular Weight 14594.90 Da.
    Residues 132 Isoelectric Point 5.75
    Sequence mkgvieyslktsnddqfiditnlvkkavdesgvsdgmavvfcphttagitinenadpdvtrdilvnldk vfpkvgdykhvegnshahikaslmgssqqiiiengklklgtwqgiyftefdgprdrkvfvkii
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.31 Rfree 0.18503
    Matthews' coefficent 1.87 Rfactor 0.1574
    Waters 159 Solvent Content 33.86

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vmh
    1. Sensitive genome-wide screen for low secondary enzymatic activities: the YjbQ family shows thiamin phosphate synthase activity
    E Morett, G Saab-Rincn, L Olvera, M Olvera - Journal of molecular , 2008 - Elsevier
     
    2. Post to
    A Paiardini, R Sali, F Bossa - BMC structural , 2008 - biomedcentral.com
     
    3. Quantum Chemical Investigations on Intraresidue Carbonyl_ Carbonyl Contacts in Aspartates of High-Resolution Protein Structures
    TK Pal, R Sankararamakrishnan - The Journal of Physical , 2009 - ACS Publications
     
    4. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    The gene CA_C0907 from Clostridium acetobutylicum encodes the NP_347543 protein belonging to the UPF0047 group ( PF01894). Its neighboring gene, CA_C0906 encodes an alanyl-tRNA synthetase related protein.

    SCOP classifies 1vmh in the alpha+beta class, YjbQ-like (super)family. DALI top hit is with PDB:1vmf (Z=23).

    The structures of several homologues of this protein have been solved: PDB:1xbf (98% id, Z=25), PDB:1ve0 (Z=20), PDB:2p6h, (Z=20), PDB:1vph (Z=21).  The protein with PDB accession code 1vph has been annotated on TOPSAN as dodecin-like protein.  This structure entry represents a domain from the full-length protein. 

    Ligand Summary



    References

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