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3dfe

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

    Title Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA VARIABILIS ATCC 29413 at 2.35 A resolution. To be published
    Site JCSG
    PDB Id 3dfe Target Id 378258
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS7067,YP_323533.1, 92728 Molecular Weight 11985.10 Da.
    Residues 110 Isoelectric Point 7.64
    Sequence mskranklvivtekvllkkvakiieeagatgytvvdtggkgsrnvrstgkpntsdtdsnvkfevltenr emaekiadqvaikfftdyagiiyiceaevlygrtfcgpdgc
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.35 Rfree 0.267
    Matthews' coefficent 2.21 Rfactor 0.224
    Waters 21 Solvent Content 44.32

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3dfe
    1. The Ising model for prediction of disordered residues from protein sequence alone
    MY Lobanov, OV Galzitskaya - Physical Biology, 2011 - iopscience.iop.org
     
    2. The extra-membranous domains of the competence protein HofQ show DNA-binding, flexibility and a shared fold with type-I KH-domains
    M Tarry, M Jskelinen, A Paino, H Tuominen - Journal of Molecular , 2011 - Elsevier
     
    3. Structural Underpinnings of Nitrogen Regulation by the Prototypical Nitrogen-Responsive Transcriptional Factor NrpR
    G Wisedchaisri, DM Dranow, TJ Lie, JB Bonanno - Structure, 2010 - Elsevier
     
    4. PII signal transduction proteins: nitrogen regulation and beyond
    LF Huergo, G Chandra - FEMS Microbiology , 2012 - Wiley Online Library
     
    5. A New Library of Surface Patches: Design and Applications
    R Gamliel, K Kedem, R Kolodny, C Keasar - 2009 - cs.bgu.ac.il
     

    Protein Summary

    THIS IS A CASP8 TARGET. DO NOT UPLOAD PROTEIN IMAGES ON THIS PAGE. PAGE PERMISSION RESTRICTED TO JCSG REFINERS.

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    JCSG Structure Refinement Summary

    There are 6 protomers per asymmetric unit of the crystal lattice. Crystal packing analysis suggests a trimer to be the oligomeric form in solution. Size Exclusion Chromatography coupled with Static Lightforming supports the assignment of a trimer as the significant solution state oligomer as shown below:

    JCSG Structure Refinement Summary

    No putative conserved domains are detected in the Conserved Domain Database. JCSG Structure Refinement Summary


    PSI-BLAST produces hits to hypothetical proteins and Nitrogen Regulatory Protein P-II (GlnB/GlnK) from many organisms ranging from 77% sequence id (exp=1e-46) to 31% seq id. Structure of closest sequence homolog is 2CZ4.pdb with 31% seq id (Ref 1).
    JCSG Structure Refinement Summary

    According to JCSG/TVPC, low similarity PDB homologs are 2CZ4 (28% id, 88% covp)
    By JCSG/FFAS, 2CZ4.pdb, 1UL3, 2GNK, 1PIL, etc are the top hits.

    JCSG Structure Refinement Summary

    Superimposition of this protein on the 2CZ4.pdb (in cyan below) and 2GNK (GlnK, a PII-homolog, yellow monomer, Ref2):




    JCSG Structure Refinement Summary

    The proteins are similar in structure, but there is difference in the relative positions of the protomers in this structure as compared to 2CZ4.



    JCSG Structure Refinement Summary

    JCSG Structure Refinement Summary

    Superimposition of the monomer of this protein (red) on the ATP-bound monomer from 2GNK (yellow, Ref 2) is shown below.

    There is a Tyr32 in this protein from a neighboring protomer that is close to the ATP molecule purine ring in this model.


    Ligand Summary

    JCSG Structure Refinement Summary

    JCSG Structure Refinement Summary

    None. Solvent structure has IPA and EDO.

    Reviews

    References

     

    No references found.

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