The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of an uncharacterized conserved protein of COG5646 (ZP_00384875.1) from Lactobacillus casei ATCC 334 at 1.69 A resolution. To be published
    Site JCSG
    PDB Id 2i8d Target Id 368040
    Molecular Characteristics
    Source Lactobacillus casei atcc 334
    Alias Ids TPS1531,YP_807469.1, BIG_25, BIG_439, 90870 Molecular Weight 14434.85 Da.
    Residues 122 Isoelectric Point 6.50
    Sequence mgslaewyqriptpddltrveslfanmqaqfpqlklefkwnqpmftdhgtfimgfnpskkhlavaiepq tmtrfipqidkagydhsqiirfpwhkpldeqlihdliaytidqkkdattfwqr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.69 Rfree 0.197
    Matthews' coefficent 2.56 Rfactor 0.168
    Waters 307 Solvent Content 51.90

    Ligand Information


    Google Scholar output for 2i8d
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
    3. The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of _+ _ fold
    S Wang, O Kirillova, M Chruszcz, D Gront - Protein , 2009 - Wiley Online Library

    Protein Summary

    Gene LSEI_2283 from Lactobacillus casei atcc 334 codes for the YP_807469 protein that belongs to the DUF1801 group (PF08818). The YP_807469 protein shows homology to uncharacterized conserved proteins from COG5646.

    2i8d is structurally similar to 2oc6 (rmsd 1.5 Å over 81 residues, 49% sequence id; Z=9.3) and 2kl4 (Z=7.6). Weaker similarity is found with type II and II secretion chaperones from bacterial pathogens (2bsi from Yersinia pestis, 1ry9 from Shigella flexneri; Z=2.5) and a SARS coronavirus proteinase (2a1v; Z=2.6). 2r6u also shows some structural similarity (rmsd 4 Å over 60 residues, 8% sequence id; Z=2.0).

    Analysis of the crystallographic packing of 2i8d using the PQS server {Henrick, 1998 #73} indicates that a dimer is the biologically relevant form. 2i8d has unknown ligand modeled in a cleft created by residues from chain A (Trp40, Ala65, and Arg90) and chain B (Asp84, His85, Ser86, Trp120, and Arg122).

    A functional similarity of DUF1801 members to the frataxin family supporting a general cellular role for frataxin-type proteins in cellular iron homeostasis has been proposed [Ref].

    Ligand Summary





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