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1o13

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

    Title Crystal structure of probable NifB protein that is involved in FeMo-Co biosynthesis TM1816 from Thermotoga maritima at 1.83 A resolution. To be published
    Site JCSG
    PDB Id 1o13 Target Id 283669
    Related PDB Ids 1t3v 
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1317,TM1816, 89497 Molecular Weight 13624.70 Da.
    Residues 124 Isoelectric Point 6.18
    Sequence miiaipvsenrgkdspisehfgrapyfafvkvknnaiadisveenplaqdhvhgavpnfvkekgaelvi vrgigrraiaafeamgvkvikgasgtveevvnqylsgqlkdsdyevhdhhhhehh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.83 Rfree 0.241
    Matthews' coefficent 2.20 Rfactor 0.207
    Waters 96 Solvent Content 43.55

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o13
    1. Assessment of homology_based predictions in CASP5
    A Tramontano, V Morea - Proteins: Structure, Function, and , 2003 - Wiley Online Library
     
    2. Can molecular dynamics simulations provide high_resolution refinement of protein structure?
    J Chen, CL Brooks III - Proteins: Structure, Function, and , 2007 - Wiley Online Library
     
    3. Finding functional sites in structural genomics proteins
    A Stark, A Shkumatov, RB Russell - Structure, 2004 - Elsevier
     
    4. Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins
    I Ovidiu, O Numan, VS Mathura - Current medicinal , 2004 - ingentaconnect.com
     
    5. A new generation of statistical potentials for proteins
    Y Dehouck, D Gilis, M Rooman - Biophysical journal, 2006 - Elsevier
     
    6. CASP5 target classification
    LN Kinch, Y Qi, TJP Hubbard - : Structure, Function, and , 2003 - Wiley Online Library
     
    7. Local quality assessment in homology models using statistical potentials and support vector machines
    M Fasnacht, J Zhu, B Honig - Protein science, 2007 - Wiley Online Library
     
    8. Refining homology models by combining replica_exchange molecular dynamics and statistical potentials
    J Zhu, H Fan, X Periole, B Honig - : Structure, Function, and , 2008 - Wiley Online Library
     
    9. Lattices for ab initio protein structure prediction
    CL Pierri, A De Grassi, A Turi - Proteins: Structure, Function, , 2008 - Wiley Online Library
     
    10. Sampling of near_native protein conformations during protein structure refinement using a coarse_grained model, normal modes, and molecular dynamics simulations
    AW Stumpff_Kane, K Maksimiak - Proteins: Structure, , 2008 - Wiley Online Library
     
    11. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    12. CASP9 target classification
    LN Kinch, S Shi, H Cheng, Q Cong, J Pei - Proteins: Structure, , 2011 - Wiley Online Library
     
    13. SPIStructure predictability index for protein sequences
    M Brylinski, L Konieczny, I Roterman - Silico Biol, 2004 - bioinfo.de
     
    14. A fold-recognition approach to loop modeling
    C Levefelt, D Lundh - Journal of molecular modeling, 2006 - Springer
     
    15. A seqlet-based maximum entropy Markov approach for protein secondary structure prediction
    Q Dong, X Wang, L Lin, Y Guan - Science in China Series C: Life Sciences, 2005 - Springer
     
    16. NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima
    L Columbus, W Peti, T Etezady_Esfarjani - Proteins: Structure, , 2005 - Wiley Online Library
     
    17. NMR structure of the protein NP_247299. 1: comparison with the crystal structure
    K Jaudzems, M Geralt, P Serrano - Section F: Structural , 2010 - scripts.iucr.org
     
    18. Evaluating the solution from MrBUMP and BALBES
    RM Keegan, F Long, VJ Fazio, MD Winn - Section D: Biological , 2011 - scripts.iucr.org
     
    19. Conformational Sampling in Structure Prediction and Refinement with Atomistic and Coarse-Grained Models
    M Feig, SM Gopal, K Vadivel - Multiscale Approaches to , 2011 - Springer
     
    20. Protein Structure Prediction Using an Augmented Homology Modeling Method: Key Importance of Iterative-Procedures for Obtaining Consistent Quality Models
    S McDonald, S Mylvaganam - Current , 2005 - ingentaconnect.com
     
    21. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     
    22. Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas
    S Najmudin, C Bonifacio, AG Duarte - Section F: Structural , 2009 - scripts.iucr.org
     
    23. Local descriptors of protein structure: A systematic analysis of the sequence_structure relationship in proteins using short_and long_range interactions
    TR Hvidsten, A Kryshtafovych - : Structure, Function, and , 2009 - Wiley Online Library
     
    24. SPI-Structure Predictability Index for Protein Sequences
    M Brylinski, L Konieczny, I Roterman - In silico biology, 2005 - IOS Press
     
    25. Integrated software environment for protein structure refinement
    R Ravindrudu, D Wu, A Guaratne - , 2008. BIBMW 2008. , 2008 - ieeexplore.ieee.org
     

    Protein Summary

    The gene TM1816 from Thermotoga maritima encodes a putative dinitrogenase iron-molybdenum cofactor PF02579. This conserved domain belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.  The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily SCOP53146.

    Ligand Summary


    References

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