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The Open Protein Structure Annotation Network
PDB Keyword
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2inb

    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 2inb Target Id 368168
    Molecular Characteristics
    Source Nostoc punctiforme pcc 73102
    Alias Ids TPS1535,NPUN_22DEC03_CONTIG1_REVISED_GENENPF2941, BIG_35, 86482 Molecular Weight 15903.53 Da.
    Residues 139 Isoelectric Point 5.44
    Sequence msakdvfhqvvkialekdgwqitndpltisvggvnlsidlgaekliaaeregekiavevksflerssai sefhtalgqfinyrgalrrrqpervlylavplttyktffqldfpkemiaenqvkmliydveqevifqwin
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.191
    Matthews' coefficent 2.27 Rfactor 0.158
    Waters 137 Solvent Content 45.86

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2inb
    1. Image-based crystal detection: a machine-learning approach
    R Liu, Y Freund, G Spraggon - Acta Crystallographica Section D: , 2008 - scripts.iucr.org
     

    Protein Summary

    Nostoc punctiforme hypothetical protein Npun02006528 (Zp_00107633) represents a family of recombination directionality factors (RDFs) from nitrogen fixing bacteria. It is a first structure from this family, shows unexpected structural similarity to endonucleases, despite low sequence similarity (~12% seq id).


    It has the highest structural similarity to PDB structures 1y88 (DALI Z-score 8.6; RMSD 3.0; 14% sequence identity for 104 superimposed residues), 1xmx (DALI Z-score 6.8, RMSD 3.3), 2ixs (DALI Z-score 5.9; RMSD 3.3), 1gef (DALI Z-score 5.9, RMSD 2.8), 2fok (DALI Z-score 5.8, RMSD 3.0), 2czr (DALI Z-score 5.8; RMSD 2.5).

    Analysis of the crystallographic packing using the PQS server {Henrick, 1998 #73} indicates that a dimer is the biologically relevant form.

     

    The dimer interface has a buried surface area of 1022 Angstrom squared (Delta G = -14.2 kcal/mol) as assessed by PISA server.

     

    Top Dali hits are:

     

     
    No: Chain Z rmsd lali nres %id PDB Description
    1:  2inb-A 28.2  0.0  128   128  100 PDB  MOLECULE: HYPOTHETICAL PROTEIN;                                      
       2:  2okf-A 25.8  0.9  128   129   88 PDB  MOLECULE: FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN;          
       3:  2okf-B 25.8  0.9  128   129   88 PDB  MOLECULE: FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN;          
       4:  1y88-A  9.3  2.9  105   184   14 PDB  MOLECULE: HYPOTHETICAL PROTEIN AF1548;                               
       5:  2vld-A  8.6  2.6   94   228   13 PDB  MOLECULE: UPF0286 PROTEIN PYRAB01260;                                
       6:  2vld-B  8.6  2.7   98   226   12 PDB  MOLECULE: UPF0286 PROTEIN PYRAB01260;                                
       7:  2ph7-B  8.6  2.6  100   219    9 PDB  MOLECULE: UNCHARACTERIZED PROTEIN AF_2093;                           
       8:  4g6v-A  7.6  3.3  104   132    7 PDB  MOLECULE: ADHESIN/HEMOLYSIN;                                         
       9:  2ewf-A  7.6  2.6   95   587   12 PDB  MOLECULE: NICKING ENDONUCLEASE N.BSPD6I;                             
      10:  4g6v-C  7.6  3.3  104   132    7 PDB  MOLECULE: ADHESIN/HEMOLYSIN;                                         
      11:  4g6v-G  7.6  3.4  103   132    7 PDB  MOLECULE: ADHESIN/HEMOLYSIN;                                         
      12:  4g6v-E  7.6  3.4  103   132    7 PDB  MOLECULE: ADHESIN/HEMOLYSIN;                                         
      13:  1xmx-A  7.5  3.3  109   380    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VC1899;                               
      14:  2ph7-A  7.5  2.8  100   220    8 PDB  MOLECULE: UNCHARACTERIZED PROTEIN AF_2093;                           
      15:  3dnx-A  7.2  2.7   97   146   18 PDB  MOLECULE: UNCHARACTERIZED PROTEIN SPO1766;                           
      16:  3c25-B  6.7  3.2  110   353    9 PDB  MOLECULE: NOTI RESTRICTION ENDONUCLEASE;                             
      17:  3c25-A  6.6  3.1  109   354    8 PDB  MOLECULE: NOTI RESTRICTION ENDONUCLEASE;                             
      18:  3bvr-A  6.6  3.1  109   354    8 PDB  MOLECULE: NOTI RESTRICTION ENDONUCLEASE;                             
      19:  3bvr-B  6.5  3.1  111   353    8 PDB  MOLECULE: NOTI RESTRICTION ENDONUCLEASE;                             
      20:  1d02-A  6.3  3.4  112   197    8 PDB  MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3');              
      21:  2fok-B  6.3  2.9   96   560   13 PDB  MOLECULE: FOKI RESTRICTION ENDONUCLEASE;                             
      22:  2fok-A  6.2  2.9   96   558   13 PDB  MOLECULE: FOKI RESTRICTION ENDONUCLEASE;                             
      23:  2ixs-B  6.2  3.4  102   319    2 PDB  MOLECULE: SDAI RESTRICTION ENDONUCLEASE;                             
      24:  3fov-A  6.1  3.2   78   102   17 PDB  MOLECULE: UPF0102 PROTEIN RPA0323;                                   
      25:  1fok-A  6.1  3.1   98   568   13 PDB  MOLECULE: PROTEIN (FOKI RESTRICTION ENDONUCLEAS);                    
      26:  1gef-D  6.1  2.8   82   109   17 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      27:  2ixs-A  6.0  3.4  101   319    2 PDB  MOLECULE: SDAI RESTRICTION ENDONUCLEASE;                             
      28:  2wiw-A  6.0  3.0   86   120   16 PDB  MOLECULE: HJC;                                                       
      29:  1ipi-A  6.0  3.0   84   114   15 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      30:  1gef-B  6.0  2.8   82   116   17 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      31:  1gef-E  5.9  2.8   82   114   16 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      32:  2wiw-B  5.8  3.0   82   126   17 PDB  MOLECULE: HJC;                                                       
      33:  2wcw-D  5.8  3.4   84   125   18 PDB  MOLECULE: HJC;                                                       
      34:  2wcw-C  5.8  3.1   82   121   17 PDB  MOLECULE: HJC;                                                       
      35:  1ipi-B  5.8  2.9   78   114   17 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      36:  1gef-A  5.7  2.7   78   120   18 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      37:  2p14-A  5.7  3.3  100   186   14 PDB  MOLECULE: HETERODIMERIC RESTRICTION ENDONUCLEASE R.BSPD6I S          
      38:  1ob9-A  5.7  3.2   86   124   15 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      39:  2wcz-A  5.7  3.1   82   123   17 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      40:  4f0p-D  5.7  3.3   93   452   11 PDB  MOLECULE: RESTRICTION ENDONUCLEASE;                                  
      41:  2wj0-A  5.6  3.1   82   125   17 PDB  MOLECULE: ARCHAEAL HJC;                                              
      42:  2wiz-A  5.6  3.3   84   125   18 PDB  MOLECULE: ARCHAEAL HJC;                                              
      43:  2wiz-B  5.6  3.2   84   122   18 PDB  MOLECULE: ARCHAEAL HJC;                                              
      44:  2wcw-B  5.6  3.0   81   122   17 PDB  MOLECULE: HJC;                                                       
      45:  1hh1-A  5.5  3.4   83   125   17 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVING ENZYME HJC;                    
      46:  1d02-B  5.5  3.4  104   200    8 PDB  MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3');              
      47:  2wcw-A  5.5  3.3   82   126   17 PDB  MOLECULE: HJC;                                                       
      48:  1ob8-A  5.5  2.8   80   119   16 PDB  MOLECULE: HOLLIDAY-JUNCTION RESOLVASE;                               
      49:  2wcz-B  5.5  3.1   79   113   16 PDB  MOLECULE: HOLLIDAY JUNCTION RESOLVASE;                               
      50:  2czr-A  5.5  2.4   75   226   13 PDB  MOLECULE: TBP-INTERACTING PROTEIN;                                   
    

    Ligand Summary



    References

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