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The Open Protein Structure Annotation Network
PDB Keyword
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2nlv

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

    Title Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models. Proteins 2014
    Site JCSG
    PDB Id 2nlv Target Id 367696
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS1523,YP_324325.1, BIG_57, BIG_402, 86302 Molecular Weight 13104.34 Da.
    Residues 111 Isoelectric Point 5.05
    Sequence mdklvkyqelvkklltnyasddvsdqdvevqlildternhyqwmnvgwqglnriyrcvihfdikdgkiw lqqnltdrnpaeelvmmgvpredivlglqapykrqytdygva
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.30 Rfree 0.195
    Matthews' coefficent 2.06 Rfactor 0.175
    Waters 296 Solvent Content 40.21

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2nlv
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Modeling structural heterogeneity in proteins from X-ray data
    A Dhanik, H Van Den Bedem, A Deacon - Algorithmic Foundation of , 2009 - Springer
     

    Protein Summary

    The AVA3825 gene from A. variabilis ATCC 29413 encodes the YP_324325 amino acid sequence belonging to the XisI-like proteins (fdxN element excision controlling factor protein) (PF08869). It has weak structural similarity to aldehyde oxidoreductase (PDB structure 1dgj; DALI Z-score = 5.4; RMSD = 2.3; 3% sequence identity for 59 superimposed residues). The most conserved residues are Trp48 and Trp69  (both are located next to two different  clefts).

     

    Top hits from Dali are:

     

    No: Chain Z rmsd lali nres %id PDB Description

         1:  2nlv-A 24.1  0.0  112   112  100 PDB  MOLECULE: XISI PROTEIN-LIKE;                                         
       2:  2nlv-B 21.2  0.6  109   109  100 PDB  MOLECULE: XISI PROTEIN-LIKE;                                         
       3:  3d7q-A 19.9  1.0  109   109   46 PDB  MOLECULE: XISI PROTEIN-LIKE;                                         
       4:  3d7q-B 19.6  1.4  112   112   46 PDB  MOLECULE: XISI PROTEIN-LIKE;                                         
       5:  2nwv-A 17.9  1.7  108   112   35 PDB  MOLECULE: XISI PROTEIN-LIKE;                                         
       6:  2nvm-B 17.2  1.9  109   111   31 PDB  MOLECULE: FDXN ELEMENT EXCISION CONTROLLING FACTOR XISI;             
       7:  2nvm-A 15.7  1.8  102   104   31 PDB  MOLECULE: FDXN ELEMENT EXCISION CONTROLLING FACTOR XISI;             
       8:  1soy-A  5.2  3.4   73   106    7 PDB  MOLECULE: CYAY PROTEIN;                                              
       9:  3t3l-A  4.9  3.9   77   121    9 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      10:  3s4m-A  4.9  3.8   77   121    9 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      11:  3s5f-A  4.9  3.8   77   120    8 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      12:  1ekg-A  4.9  3.9   77   119    9 PDB  MOLECULE: FRATAXIN;                                                  
      13:  3s5d-A  4.9  3.9   77   121    8 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      14:  3s5f-B  4.8  3.8   77   125    8 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      15:  3t3x-A  4.8  3.9   77   122    9 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      16:  3t3k-A  4.8  3.9   77   122    9 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      17:  3t3j-A  4.8  3.9   77   123    9 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      18:  4jpd-A  4.8  3.4   72   109    7 PDB  MOLECULE: PROTEIN CYAY;                                              
      19:  3s5e-A  4.8  3.7   77   121    8 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;                                   
      20:  3t3t-C  4.7  3.9   77   120    9 PDB  MOLECULE: FRATAXIN, MITOCHONDRIAL;     
    

    Ligand Summary



    References

    Reviews

    References

     

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