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2i51

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

    Title Crystal structure of Uncharacterized conserved protein of COG5135 (ZP_00109616.1) from Nostoc punctiforme PCC 73102 at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 2i51 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1506,NPUN_22DEC03_CONTIG1_REVISED_GENENPF5749, 2.30.110.10, 90908
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.70 Rfactor 0.165
    Waters
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    Solvent Content 54.04

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2i51
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
     

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    Protein Summary

    Gene Npun_F5749 from Nostoc punctiforme PCC 73102 encodes the YP_001868992 amino acid sequence (obsolete entry: ZP_00109616), a bacterial Riboflavin monophosphate (FMN) binding protein, but only 5 of 15 FMN-binding residues are conserved here (Arg40, Tyr58, Ser62, and two residues from the opposite chain - Gln86 and Arg88). Similar proteins are found also in fungi and Arabidopsis thaliana.

    The whole sequence of ZP_00109616 has strong similarity to uncharacterized conserved proteins from COG5135. ZP_00109616 N-terminal part is similar to Pyridoxamine 5`-phosphate oxidase protein family (Pfam01243), but neither the PLP-cofactor is present in this crystal structure, nor the lysine that would interact with this cofactor (Lys131 and Lys135 are located on a flexible loop, but their side chains are not close enough to the possible PLP-binding site in this crystal structure).

    Phylogenetic cooccurrence indicates that functions of ZP_00109616 can be interdependent with: PSBH [PSBH_ANASP] - photosystem II reaction center H protein (PSII-H), ALR0515 [Q8YZE5] - hypothetical protein Alr0515 ALL0737, and [Q8YYV6]  - thioredoxin reductase.

    Pre-SCOP classifies 2i51 in the all beta class, FMN-binding split barrel supefamily, PNP-oxidase-like family. A DALI search informs that 2i51 is structurally similar to PNP-oxidases like 1dnl (Z=19), 1t9m, 1wv4. Analysis of the crystallographic packing of 2i51 using the PQS server {Henrick, 1998 #73} indicates that a dimer is the biologically relevant form.

    Ligand Summary



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