{
"code": "SASDX24",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structure of the chromoprotein ovorubin from the golden apple snail ( Pomacea canaliculata\n )",
"publication": {
"title": "Structure of the chromoprotein ovorubin from the golden apple snail ( Pomacea canaliculata\n )",
"author_list": "Wilasluck P, Saw W, Tran B, Sabat G, Shih O, Hengphasatporn K, Shigeta Y, Vinayavekhin N, Wangkanont K",
"journal": "Protein Science",
"doi": "10.1002/pro.70439",
"pmid": null,
"published_date": "2025 Dec 23"
},
"status": "released",
"submitted_date": "2025-04-23",
"released_date": "2025-12-26"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX24.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX24.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX24_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX24_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX24_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX24_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX24.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger X 1M & 9M",
"resolution": 0.001
},
"name": "NSRRC",
"city": "Hsinchu",
"country": "Taiwan",
"beamline_name": "TPS13A",
"beam_geometry": null,
"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": "Perivitellin ovorubin-1",
"short_name": "PcOvo1",
"sequence": "PHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRLLIVIRLDAQSYEKLDEITVP\r\nGKVEVIPAVNMADTMERCGVSWPRVELTDDNVTLFESESTLTDVTKEQLKAMLIGYGE\r\nHMSGLLQAHRFEYYQAAGATPHRHFVFVNSVPDEIEVFGREGVDIWGGPGEFVVKPQY\r\nVTRI",
"organism": "Pomacea canaliculata",
"uniprot_code": "J7I2T6",
"uniprot_range_first": 20,
"uniprot_range_last": 200,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MFVATSLLLAIATLVVRASPHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRL\nLIVIRLDAQSYEKLDEITVPGKVEVIPAVNMADTMERCGVSWPRVELTDDNVTLFESEST\nLTDVTKEQLKAMLIGYGEHMSGLLQAHRFEYYQAAGATPHRHFVFVNSVPDEIEVFGREG\nVDIWGGPGEFVVKPQYVTRI",
"mw": 20.426,
"total_mw": 40.852,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Pomacea canaliculata Ovorubin 1: The 10-meric ovorubin contains two copies of each of the following proteins: PcOvo1, PcOvo2, PcOvo3s, PcOvo4-1, and PcOvo5."
},
{
"long_name": "Perivitellin ovorubin-2",
"short_name": "PcOvo2",
"sequence": "LQKHYIIYEVRNIEKTPEEVKEEMKDTDILYSFKALGAPSYHIVVEVNPRNMRKLEEVE\r\nLKGKIRMVPVVNMVDVAETLGVSWPRSGARLLDVNLTLIERTLNQEGLTSQESEAHL\r\nKGFMEELKDRLQQYNYQAFFTIGASPPKMYIYINIPYEEVDKFACIGINQFGGPAAVNT\r\nTVSFISSFPK",
"organism": "Pomacea canaliculata",
"uniprot_code": "J7HZ90",
"uniprot_range_first": 26,
"uniprot_range_last": 210,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAEHRIPVLLLLVVVAASSLAQQIPLQKHYIIYEVRNIEKTPEEVKEEMKDTDILYSFKA\nLGAPSYHIVVEVNPRNMRKLEEVELKGKIRMVPVVNMVDVAETLGVSWPRSGARLLDVNL\nTLIERTLNQEGLTSQESEAHLKGFMEELKDRLQQYNYQAFFTIGASPPKMYIYINIPYEE\nVDKFACIGINQFGGPAAVNTTVSFISSFPK",
"mw": 21.15,
"total_mw": 42.3,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Pomacea canaliculata Ovorubin 2: The 10-meric ovorubin contains two copies of each of the following proteins: PcOvo1, PcOvo2, PcOvo3s, PcOvo4-1, and PcOvo5."
},
{
"long_name": "Uncharacterized protein (ovorubin-3, short)",
"short_name": "PcOvo3s",
"sequence": "NKEYLLLDIRDATTSEIISALRDVEIELKVKAKGIARHLIVVKQNDANLQKLGEIDIPGRS\r\nCSTPVEDLDNLMEDIGISWPRNELTNVNVTLFERTLDLKDKTMEQFWSEAKAYGQLV\r\nKPVLSSFTYRAFKANGAYPPKVYFFVNLPRENLNDASSKGIDIFGGPGKARTTVQYVT\r\nKLS",
"organism": "Pomacea canaliculata",
"uniprot_code": "A0A2T7NVP5",
"uniprot_range_first": 21,
"uniprot_range_last": 194,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MYALAIALLAFSTFVSNAFANKEYLLLDIRDATTSEIISALRDVEIELKVKAKGIARHLI\nVVKQNDANLQKLGEIDIPGRSCSTPVEDLDNLMEDIGISWPRNELTNVNVTLFERTLDLK\nDKTMEQFWSEAKAYGQLVKPVLSSFTYRAFKANGAYPPKVYFFVNLPRENLNDASSKGID\nIFGGPGKARTTVQYGQAAQELLTPPEDQEVGRVGSTLRGHTGALMFVATSLLLAIATLVV\nKASPHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRLLIVIRLDAQSYEKLDE\nITVPGKVEVIPAVNMADTMERCGVSWPRVELTDDNHFVFVNSVPDEIEVFGREGVDIWGG\nPGEFVVKPQIADPAVVKRGLKGQTRSTAIVDNQTNALKMLVATLTLVALSAVFTNVYGSD\nQYTILDVYKASNVSVEDYKDLLKDLDVVHSFKVLGSSRVIFVVKMREDSYEKLSKINLPG\nDVYSIPAGDLSDKMQSVGVEWKRWDDLPDANLTLFERTLELKGEPLEGLASHMKAFGEKV\nSHVMELYPNKGFYLLGRTPPKAFVIVSLPFRCRQVRYGSDFALNYLNGPGDSSTKVEFVA\nKA",
"mw": 20.124,
"total_mw": 40.248,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Pomacea canaliculata Ovorubin 3 short: The 10-meric ovorubin contains two copies of each of the following proteins: PcOvo1, PcOvo2, PcOvo3s, PcOvo4-1, and PcOvo5."
},
{
"long_name": "Perivitellin protein (ovorubin-4, form 1)",
"short_name": "PcOvo4-1",
"sequence": "QDLVFAEWDKGSSHEHACSALRNSSVIEKGLTVKEVGTSKFAAVLSEPILARL\r\nKFHGLVEAVPVVEVGTVMKRLNVSIPPAQDISDNNLTLIKMSPKLKGQTLQQ\r\nIDAELRYLGEYMNTVLQKCSHRVYISKGTFPPKIYVFLNMPLDQIRQFYPSLD\r\nIFGGPSSTKNEISYVQILILRN",
"organism": "Pomacea canaliculata",
"uniprot_code": "A0A2T7NVP6",
"uniprot_range_first": 24,
"uniprot_range_last": 203,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MTAILALLLAMSILLPSGAVEDVQDLVFAEWDKGSSHEHACSALRNSSVIEKGLTVKEVG\nTSKFAAVLSEPILARLKFHGLVEAVPVVEVGTVMKRLNVSIPPAQDISDNNLTLIKMSPK\nLKGQTLQQIDAELRYLGEYMNTVLQKCSHRVYISKGTFPPKIYVFLNMPLDQIRQFYPSL\nDIFGGPSSTKNEISYVQILILRN",
"mw": 20.119,
"total_mw": 40.238,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Pomacea canaliculata Ovorubin 4 form 1: The 10-meric ovorubin contains two copies of each of the following proteins: PcOvo1, PcOvo2, PcOvo3s, PcOvo4-1, and PcOvo5."
},
{
"long_name": "Uncharacterized protein (ovorubin-5)",
"short_name": "PcOvo5",
"sequence": "SDQYTILDVYKASNVSVEDYKDLLKDLDVVHSFKVLGSSRVIFVVKMREDSYEKLSKI\r\nNLPGDVYSIPAGDLSDKMQSVGVEWKRWDDLPDANLTLFERTLELKGEPLEGLASH\r\nMKAFGEKVSHVMELYPNKGFYLLGRTPPKAFVIVSLPFRCRQVRYGSDFALNYLNGP\r\nGDSSTKVEFVAKA",
"organism": "Pomacea canaliculata",
"uniprot_code": "A0A2T7NVP5",
"uniprot_range_first": 419,
"uniprot_range_last": 602,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MYALAIALLAFSTFVSNAFANKEYLLLDIRDATTSEIISALRDVEIELKVKAKGIARHLI\nVVKQNDANLQKLGEIDIPGRSCSTPVEDLDNLMEDIGISWPRNELTNVNVTLFERTLDLK\nDKTMEQFWSEAKAYGQLVKPVLSSFTYRAFKANGAYPPKVYFFVNLPRENLNDASSKGID\nIFGGPGKARTTVQYGQAAQELLTPPEDQEVGRVGSTLRGHTGALMFVATSLLLAIATLVV\nKASPHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRLLIVIRLDAQSYEKLDE\nITVPGKVEVIPAVNMADTMERCGVSWPRVELTDDNHFVFVNSVPDEIEVFGREGVDIWGG\nPGEFVVKPQIADPAVVKRGLKGQTRSTAIVDNQTNALKMLVATLTLVALSAVFTNVYGSD\nQYTILDVYKASNVSVEDYKDLLKDLDVVHSFKVLGSSRVIFVVKMREDSYEKLSKINLPG\nDVYSIPAGDLSDKMQSVGVEWKRWDDLPDANLTLFERTLELKGEPLEGLASHMKAFGEKV\nSHVMELYPNKGFYLLGRTPPKAFVIVSLPFRCRQVRYGSDFALNYLNGPGDSSTKVEFVA\nKA",
"mw": 20.748,
"total_mw": 41.496,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Pomacea canaliculata Ovorubin 5: The 10-meric ovorubin contains two copies of each of the following proteins: PcOvo1, PcOvo2, PcOvo3s, PcOvo4-1, and PcOvo5."
}
],
"buffer": {
"name": "20 mM Tris, 150 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Ovorubin from the golden apple snail (Pomacea canaliculata)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "Chulalongkorn University",
"webpage": null
}
],
"contributor_name": "Kittikhun",
"contributor_surname": "Wangkanont",
"orcid": "https://orcid.org/0000-0002-7190-2955"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2025-03-26",
"storage_temperature": 4.0,
"cell_temperature": 25.0,
"exposure_time": 2.0,
"number_of_frames": 5,
"wavelength": 0.082656,
"sample_detector_distance": 5.5032,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 50.0,
"flow_rate": 0.35,
"s_min": 0.06,
"s_max": 8.61,
"total_exposure_time": null,
"seccolumn": 10
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX24_fit1_model1_img.png",
"software": "Phenix",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDX24_fit1_model1.pdb",
"model_mw": 210.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "PDB ID: 9UAJ.",
"user": 1222
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX24_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 47.767,
"p_value": 0.0,
"fit_residual_plot": "SASDX24_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDX24_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX24_fit2_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDX24_fit2_model1.cif",
"model_mw": 210.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "DAMMIN from DAMMIF aligned model cohort",
"user": 1222
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX24_fit2_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 2.282,
"p_value": 0.0,
"fit_residual_plot": "SASDX24_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDX24_fit2.fir",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of ovorubin from the golden apple snail in 20 mM Tris, 150 mM NaCl, pH 7 were collected on the TPS13A beam line at the NSRRC (Hsinchu, Taiwan) using a Eiger X 1M & 9M detector at a sample-detector distances of 0.75 m and 5.5 m and at a wavelength of λ = 0.082656 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 10 mg/ml was injected at a 0.35 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 25°C. Five successive 2 second 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.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 234.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 250.0,
"porod_mw_error": null,
"pddf_i0": 0.7782,
"pddf_i0_error": null,
"guinier_i0": 0.776586,
"guinier_i0_error": null,
"pddf_rg": 4.12,
"pddf_rg_error": null,
"guinier_rg": 4.146,
"guinier_rg_error": 0.038,
"pddf_dmax": 12.4,
"pddf_dmax_error": null,
"porod_volume": 400.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 113,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDX24_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-12-26T13:07:06.341118+01:00",
"bragg_peak": []
}