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3u1w

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

    Title Crystal structure of a Hypothetical PERIPLASMIC PROTEIN (BDI_1975) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3u1w Target Id 394691
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25344,YP_001303332.1, 325982 Molecular Weight 28685.47 Da.
    Residues 252 Isoelectric Point 4.15
    Sequence ddhqgiiplppvenafqekypdaknpvfeiegnyyvvdfnnggsettawftdqgiwmmekidisfaqlp aavstafkqsfysnwtvddtyainrlnmgivykieaeqsnsevdlyysqygnlikavddeinndapivi pkevsnlmeitfanaelldiqqnslgyeldmidnqiykvaqlnkdyrwqsttwamseqevpqivmqgfe ssayasdkvqsiytllnangtfylfkvshngqdktitfdvfgniv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.00 Rfree 0.2147
    Matthews' coefficent 4.33 Rfactor 0.1893
    Waters 829 Solvent Content 71.57

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Update: This builds to overlap with DUF2874, PF11396. There are several structures for this family, eg, 3elg, listed in TOPSAN as being a structure related to BLIP, but of unknown function.

     

    A sequence search of Pfam shows that target id 39461 belongs to the DUF2874 (Pfam 11396) family. Shown below is a ribbons representation of the structure color coded with the N-terminal end in blue and the C-terminal end in red.

     

    monomer.png

    Inspection of the structure shows that it consists of two duplicated domains. Residues 29-153 comprises an N-terminal domain and residues 165-277 comprises a C-terminal domain. There are three other JCSG structures belonging to this Pfam family. These include PDB ID 3elg, PDB ID 3due, and PDB ID 3db7. Each of the two sub-domains consists of an eight-stranded beta sheet flanked at the ends by an alpha-helices. Closer examination of the structure reveals that each sub-domain can be further sub-divided into two closely interacting  BLIP-like domains. Thus, the entire monomer can be considered to consist of four tandem repeats of individual domains. The structure represents the first for this type of domain organization.

     

     

    PDB ID DALI Z-Score rmsd (Ang) length of alignment number of residues in related structure % sequence id description
    3elg-A 7.5 2.5 67 127 13 putative periplasmic protein of unknown function (YP_001299723.1) from Bacteroides vulgatus ATCC 8482 at 1.64 A resolution
    2e2u 6.8 6.2 75 620 11 Substrate Schiff-base analogue of copper amine oxidase from Arthrobacter globiformis formed with 4-hydroxybenzylhydrazine
    1iqx 6.6 2.9 68 620 12 CRYSTAL STRUCTURE OF COBALT-SUBSTITUTED AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS
    2yx9 6.6 6.2 74 620 11 Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis
    1iqy 6.5 6.1 74 620 11 CRYSTAL STRUCTURE OF NICKEL-SUBSTITUTED AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS
    3db7 6.4 2.5 60 127 18 Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution
    2cg0 6.4 6.0 74 620 11 AGAO IN COMPLEX WITH WC9A (RU-WIRE INHIBITOR, 9-CARBON LINKER, DATA SET A)
    3due 6.3 2.6 60 127 12 PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION
    2gu3 5.7 2.0 50 128 6 YpmB protein from Bacillus subtilis
    1yvb 5.5 2.8 64 111 9 the Plasmodium falciparum Cysteine Protease Falcipain-2
    1cew 5.5 2.6 64 108 9 THE 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF CHICKEN EGG WHITE CYSTATIN AND ITS POSSIBLE MODE OF INTERACTION WITH CYSTEINE PROTEINASES
    3nx0 5,5 2.7 63 109 13 Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C

    Ligand Summary

    Reviews

    References

     

    No references found.

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