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The Open Protein Structure Annotation Network
PDB Keyword
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2pgc

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

    Title Crystal structure of uncharacterized protein (JCVI_PEP_1096685590403) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 2.53 A resolution. To be published
    Site JCSG
    PDB Id 2pgc Target Id 367457
    Molecular Characteristics
    Source Unknown
    Alias Ids TPS1511,JCVI_PEP_1096685590403 Molecular Weight 22963.94 Da.
    Residues 206 Isoelectric Point 6.83
    Sequence msninyviltvasvdfsyretmarlmssyskdlidnagakgtrfgsigtgdhagslifiqfyddltgyq kaleiqskssvfkeimdsgkaniylrnistslptkfeqsyehpkyivltraeaamsdkdkflncindta scfkdngaltlrfgnlltgsnvgnyllgvgypsmeaiektydellahssykelmtfakvnmrniikil
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 5
    Resolution (Å) 2.53 Rfree 0.246
    Matthews' coefficent 2.50 Rfactor 0.214
    Waters 131 Solvent Content 50.72

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2pgc
    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. Probing metagenomics by rapid cluster analysis of very large datasets
    W Li, JC Wooley, A Godzik - PLoS One, 2008 - dx.plos.org
     
    3. Metagenomics and the protein universe
    A Godzik - Current opinion in structural biology, 2011 - Elsevier
     

    Protein Summary

    JCVI_PEP_1096685590403 is a hypothetical protein without any significant homology to any current member in the Pfam database.

    Analysis of 2pgc structure shows the presence of two repeated domains (from positions 1 to 90 and 120-206). Each polypeptide chain chelates a Cl ion via residues Y179 and R200 of the C-terminal repeat. SCOP classifies it into the alpha+beta class, ferredoxin-like fold, dimeric alpha+beta barrel superfamily, marine metagenome DABB3 family. Significant structural similarity (FFAS scr=-19; HHpred P-val=1.7e-10; Dali Z-scr=18.7) is detected with 3f44, a putative mono-oxygenase. A close second hit (Dali Z-scr=17.2; FATCAT P-val=5e-7) is with 2cb2, a sulfur oxygenase reductase (SOR) [Ref]. Another structurally similar protein is 3bxv [Ref] (Z=16.8), sharing 87% sequence identity with 2cb2. The active site of this 3bxv was identified by mutational experiments as Cys-31, Cys-101, and Cys104 and a metal ligation site at residues His-86, His-90, and Glu-114. None of these residues is conserved in a structural alignment between 2pgc and 3bxv. Therefore, a functional assignment from 3bxv cannot be inferred.

    Ligand Summary



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