Dipeptidyl peptidase III: pgDPP3_FL

{
  "code": "SASDC58",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain.",
    "publication": {
      "title": "A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain.",
      "author_list": "Hromić-Jahjefendić A, Jajčanin Jozić N, Kazazić S, Grabar Branilović M, Karačić Z, Schrittwieser JH, Das KMP, Tomin M, Oberer M, Gruber K, Abramić M, Tomić S",
      "journal": "PLoS One",
      "doi": "10.1371/journal.pone.0188915",
      "pmid": "29190734",
      "published_date": "2017"
    },
    "status": "released",
    "submitted_date": "2017-10-09",
    "released_date": "2017-12-12"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC58.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC58.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC58_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC58_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC58_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC58_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC58.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Peptidase, M49 family",
          "short_name": "PgDPP3",
          "sequence": "MTKETTQHRSGERVARFADIEVLSYRADLFGTLTPKQRMLCYHLSEAALRGRDITTIQNCRYNLWVRSLMERIYTHLSKSERTDDFALLEEYLFCIWFANGIHHHYSGAKFIARFSPEFLREALRVTGVELEPEEQALLERVLYDTDFLPKQTEQSGEEDIIKASSVNFYAPGITRAEAESHYKNLIEALPENERSCPPSFGLNTRLIRSTSGELKDEVCCIDGLYSPAIEAVVASLEAAIPYTENEEQAACIRLLCDYYRTGDVRLYDRFCIRWVENNRTRIDFINGFTEVYADPIGIHGSWEGLVHMQDEEAGRRTRIISEHAGWFEAHSPIDARFRKKNPHGISATVVNVLTIAGDSYPATPIGINLPNADWIRAEHGSKSVTIDNITDAYNHAARGTGLYEEFIPDEEVRRHVELHADLTDSLHTDLHECLGHGSGQLLPGVPGDALGEHASTLEETRADLFALYFLADPKMIELGLLTDPDAYKANYYKYMLNGLMTQLVRIKRGEEIEEAHMRNRALIARYVLEHAERPGAMSLVCEEGKTALVIKDYEAVRAIIAGLLTEVQRIKSEGDYTAGKALVERYAVHVDPLLHEEVLMRYAKLDIAPYKGFVNPRLRPVYNSEGRLTDATIEYTEGYAEQMLRYSAEYSFLPTDSPLLQEARRLRSHLRRAMDGVLSASMREKGLHYGINFGVTREHLLRLARTADASAPLADYLWRRDVRETKILATMIFPAEELTHEQATRFLREADNVELREQLTANLLERMPEAIRSIGRWIESKETTPDMMTGVLTLAARLFTRGIFPENAPAEKLLALAILHLSDEEQKTELRRASALLLKRYGRGSAERTKKVLCLLPESSQDTAPVLYELCEDIRFELDFYPKDEHHHHHH",
          "organism": "Porphyromonas gingivalis",
          "uniprot_code": "Q7MX92",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTKETTQHRSGERIARFADIEVLSYRADLFGTLTPKQRMLCYHLSEAALRGRDITTIQNC\nRYNLWVRSLMERIYTHLSKSERTDDFALLEEYLFCIWFANGIHHHYSGAKFIARFSPGFL\nRAALREAGVELEPEEQVLLERVLYDTDFLPKQTEQSGEEDIIKASSVNFYAPGITRAEAE\nSHYKNLIEALPENEKSCPPSFGLNTRLIRSTSGELKDEVCCIDGLYGPAIEAVVASLEAA\nIPYTENEEQAACIRLLCDYYRTGDIRLYDRFCIRWVENNRTRIDFINGFTEVYADPIGIH\nGSWEGLVHMQDEEAGRRTRIISEHAGWFEAHSPIDARFRKKNPHGISATVVNVLTIAGDS\nYPATPIGINLPNADWIRAEHGSKSVTIDNITDAYNHAARGTGLYEEFIPDEEVRRHVELH\nADLTDSLHTDLHECLGHGSGQLLPGVPGDALGEHASTLEETRADLFALYFLADPKMIELG\nLLTDPDAYKANYYKYMLNGLMTQLVRIKRGEEIEEAHMRNRALIARYVLEHAERPGAMSL\nVCEEGKTALVIKDYEAVRAIIAGLLTEVQRIKSEGDYTAGKALVERYAVHVDPLLHEEVL\nTRYAKLDIAPYKGFVNPRLRPVYNSEGRLTDATIEYTEGYAEQMLRYSAEYSFLPTDSPL\nLQEARRLRSHLRRAMDGVLSASMREKGLHYGINFGVTREHLLRLARTADASAPLADYLWR\nRDVRETKILATMIFPAEELTHEQATRLLREADNVELREQLTANLLERMPEAIRSIGRWIE\nSKETTPDMMTGVLTLAARLFTRGIFPEDVPAEKLLTLAILHLSDEEQKAELRRASALLLK\nRYGRGSAERTKKVLCLLPESSQDTAPVLYELCEDIRFELDFYPKDE",
          "mw": 101.655,
          "total_mw": 101.655,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50mM Tris,100mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Dipeptidyl peptidase III: pgDPP3_FL",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Graz, Austria",
            "full_name": "University of Graz",
            "webpage": "https://www.uni-graz.at"
          }
        ],
        "contributor_name": "Krishna Mohan",
        "contributor_surname": "Padmanabha Das",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-03-14",
    "storage_temperature": 4.0,
    "cell_temperature": 4.0,
    "exposure_time": null,
    "number_of_frames": 8,
    "wavelength": 0.099,
    "sample_detector_distance": 2.5,
    "concentration_min": 1.02,
    "concentration_max": 8.8,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.133,
    "s_max": 4.819,
    "total_exposure_time": null,
    "seccolumn": null
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  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC58_fit1_model1_img.png",
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          "software_version": "",
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          "model_mw": 62.63,
          "bead_radius": 3.4,
          "log": "https://www.sasbdb.org/media/log_files/pgDPP3_1.log",
          "symmetry": "",
          "comment": "",
          "user": 244
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC58_fit1_fit_img.png",
      "software": "DAMMIN",
      "chi_square_value": 0.636,
      "p_value": 0.052255,
      "fit_residual_plot": "SASDC58_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC58_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pgDPP3_1.log",
      "software_version": "",
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Dipeptidyl peptidase III: pgDPP3_FL in 50mM Tris,100mM NaCl, pH 8, were collected on the BM29 beam line at the  ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.5 m (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.0 and 8.8 mg/ml were measured . Eight successive frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
  "tags": [],
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  "guinier_rg_error": 0.018,
  "pddf_dmax": 11.25,
  "pddf_dmax_error": null,
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  "porod_volume_error": null,
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  "estimated_volume_error": null,
  "guinier_point_first": 22,
  "guinier_point_last": 64,
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  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
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