Targets - CASP13

Sequence Name:	T0964
Target:
Sequence(s):	>CBM56 NVPVTGVTVNPTTAQVEVGQSVQLNASVAPSNATNKQVTWSVSGSSIASVSPNGLVTGLAQGTTTVTATTADGNKAASATITVAPAPSTVIVIGDEVKGLKKIGDDLLFYVNGATFADLHYKVNNGGQLNVAMAPTGNGNYTYPVHNLKHGDTVEYFFTYNPGQGALDTPWQTYVHGVTQGTPE
Comments:	This is a FRET data-assisted modeling target. <br> This data type is new in CASP. Results will not be competitively assessed in CASP13. Rather, with this target we are initiating a discussion and allowing for a learning experience with the development of future FRET-based modeling techniques in mind. We are providing ample time to model this target with the closing date of September 30 (pending approval from the structure's author).<br> The molecule’s two domains seem open to homology modeling but the relative domain orientation is not known (we have the structure of only the second of the two domains starting with the residues VIVIGDE). The FRET data suggest that there may be a distribution of domain orientations, opening a challenge of dynamic modeling in CASP. This topic will be discussed at the CASP13 meeting. <p> The description of the FRET data and an overview of the results for this particular target can be found at http://predictioncenter.org/casp13/doc/FRET_CASP13_AGSeidel.pdf .<br> The detailed FRET data will be released progressively as they become available.
Subunit(s):	1
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Release date:	Today Tomorrow Day After Tomorrow Next Monday
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Sequence summary:	Sequence TSID: 76 Target: T0964 SEQUENCE : >CBM56 NVPVTGVTVNPTTAQVEVGQSVQLNASVAPSNATNKQVTWSVSGSSIASVSPNGLVTGLAQGTTTVTATTADGNKAASATITVAPAPSTVIVIGDEVKGLKKIGDDLLFYVNGATFADLHYKVNNGGQLNVAMAPTGNGNYTYPVHNLKHGDTVEYFFTYNPGQGALDTPWQTYVHGVTQGTPE NUMBER_OF_AA : 184 REAL_NUMBER_OF_AA : 184 SGI_CENTER : Others OLIGOMERIC_STATE : BINDING_SITES : LIGANDS : STOICHIOMETRY : A1 DISORDER : SOLVENT : PROTEIN_MATERIAL : YES EXPRESSION : BLAST_INFO : HHSEARCH_INFO : DIFFICULTY : Other info : From Shabir: CBM56 - a Carbohydrate Binding Module from a beta-1,3-glucanase _Bacillus circulans_ - 694 to 877 (184 aa) of Sequence ID: AAC60453.1 Length: 877. We tried to solve the structure of both parts of the CBM56, got crystals and some data, but weren_t able to solve it. So we took the second part - CBM56b and used SeMet-derivatised crystals to solve it. So this CBM56b would be the target and I am attaching the pdb for it. However, I thought it would be more interesting to see if the predictors could try modelling the whole thing and see if they can get sensible arrangements for the two parts - solved (CBM56b) and unsolved (CBM56a). These are the sequences: _ CBM56 - complete NVPVTGVTVNPTTAQVEVGQSVQLNASVAPSNATNKQVTWSVSGSSIASVSPNGLVTGLAQGTTTVTATTADGNKAASATITVAPAPSTVIVIGDEVKGLKKIGDDLLFYVNGATFADLHYKVNNGGQLNVAMAPTGNGNYTYPVHNLKHGDTVEYFFTYNPGQGALDTPWQTYVHGVTQGTPE _ CBM56_A NVPVTGVTVN PTTAQVEVGQ SVQLNASVAP SNATNKQVTW SVSGSSIASV SPNGLVTGLA QGTTTVTATT ADGNKAASAT ITVAPAPSTV IVIGD _ CBM56_B VIVIGDEVKGLKKIGDDLLFYVNGATFADLHYKVNNGGQLNVAMAPTGNGNYTYPVHNLKHGDTVEYFFTYNPGQGALDTPWQTYVHGVTQGTPE At first we thought the whole sequence was one complete thing, but on closer analysis we realised that it_s probably two independent tandem CBM modules. Even though we got crystals of the protein with both modules i.e. CBM56a and b, there is probably a flexible linker between them and the arrangement between the two modules is not homogeneous in the crystals. Hence we didn_t get good data to be able to solve it. I haven_t looked at it in great detail recently so am a bit hazy about it, but I think the modules should be homologous and both should have a similar structure to the one we have solved (CBM56b). So the interest would be to see if they are likely to pair up or be totally flexible and be independent.