Collagenase ColG s2s3as3b at pCa 3 (second analysis)

{
  "code": "SASDD63",
  "status": "Published",
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  "project": {
    "title": "Ca2+ - Induced Structural Change of Multi-Domain Collagen Binding Segments of Collagenases ColG and ColH from Hathewaya histolytica",
    "publication": {
      "title": "Ca2+ - Induced Structural Change of Multi-Domain Collagen Binding Segments of Collagenases ColG and ColH from Hathewaya histolytica",
      "author_list": "Christopher E Ruth",
      "journal": "University of Arkansas Dissertation",
      "doi": null,
      "pmid": null,
      "published_date": "2018 December"
    },
    "status": "released",
    "submitted_date": "2017-06-02",
    "released_date": "2019-08-07"
  },
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD63.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus3 X 2M",
        "resolution": 172.0
      },
      "name": "Advanced Light Source (ALS)",
      "city": "Berkeley, CA",
      "country": "USA",
      "beamline_name": "12.3.1 (SIBYLS)",
      "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,
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      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Collagenase ColG segement s2s3as3b",
          "short_name": "s2s3as3b",
          "sequence": "GSPGIPGTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEANGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIASGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK",
          "organism": "Hathewaya histolytica",
          "uniprot_code": "Q9X721",
          "uniprot_range_first": 787,
          "uniprot_range_last": 1118,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MKKNILKILMDSYSKESKIQTVRRVTSVSLLAVYLTMNTSSLVLAKPIENTNDTSIKNVE\nKLRNAPNEENSKKVEDSKNDKVEHVKNIEEAKVEQVAPEVKSKSTLRSASIANTNSEKYD\nFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTA\nNDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDE\nVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGA\nAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIV\nQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNG\nTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYK\nFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWG\nQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKSILGYLAKDKVDHRYSLKKTLNSGYD\nDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNH\nIQELADKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTL\nRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDV\nVFHGVLTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGAT\nSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEA\nNGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIA\nSGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKAT\nVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITY\nGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK",
          "mw": 37.2,
          "total_mw": 37.2,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "10mM HEPES 100mM NaCl 0.2mM EGTA",
        "concentration_unit": null,
        "comment": "pCa 3",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Collagenase ColG s2s3as3b at pCa 3 (second analysis)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Fayetteville, AR, USA",
            "full_name": "University of Arkansas",
            "webpage": "https://www.uark.edu/"
          }
        ],
        "contributor_name": "Christopher",
        "contributor_surname": "Ruth",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-10-11",
    "storage_temperature": null,
    "cell_temperature": 10.0,
    "exposure_time": 0.3,
    "number_of_frames": 33,
    "wavelength": 0.1127,
    "sample_detector_distance": 1.5,
    "concentration_min": 1.0,
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    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.125,
    "s_max": 5.413,
    "total_exposure_time": null,
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      "models": [
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          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD63_fit1_model1_img.png",
          "software": "DAMFILT",
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          "model_mw": 46.147,
          "bead_radius": 2.75,
          "log": null,
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          "comment": null,
          "user": 222
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      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD63_fit1_fixed_fit_img.png",
      "software": "DAMMIF",
      "chi_square_value": 1.892,
      "p_value": 0.261092,
      "fit_residual_plot": "SASDD63_fit1_fitresiduals_img.png",
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  "estimated_volume_method": null,
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  "pddf_software_version": "5.0",
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  "description": "In addition, refer to the related SASBDB entry SASDCS4.",
  "experiment_description": "Synchrotron SAXS data from solutions of Collagenase ColG s2s3as3b at pCa 3 in 10mM HEPES 100mM NaCl 0.2mM EGTA, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 1 and 3 mg/ml were measured at 10°C. 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 concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve. The model represents the averaged spatial representation of the protein (DAMFILT occupancy and volume-corrected bead model).",
  "tags": [],
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  "pddf_dmax": 14.35,
  "pddf_dmax_error": null,
  "porod_volume": 61.2,
  "porod_volume_error": null,
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  "estimated_volume_error": null,
  "guinier_point_first": 19,
  "guinier_point_last": 56,
  "pddf_point_first": null,
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  "symmetry": null,
  "last_modified": "2023-11-09T11:24:19.162281+01:00",
  "bragg_peak": []
}

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