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{
"code": "SASDXF5",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Recombinant expression and purification of Plasmodium heme detoxification protein in E. coli: Challenges and discoveries.",
"publication": {
"title": "Recombinant expression and purification of Plasmodium heme detoxification protein in E. coli: Challenges and discoveries.",
"author_list": "Singh R, Makde RD",
"journal": "Protein Expr Purif",
"doi": "10.1016/j.pep.2025.106789",
"pmid": "40759288",
"published_date": "2025 Aug 7"
},
"status": "released",
"submitted_date": "2025-06-12",
"released_date": "2025-08-13"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXF5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXF5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXF5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXF5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "CCD",
"name": "1D Mythen2 R series and 2D EIGER R series HPC dete",
"resolution": 73.0
},
"name": "Chemistry Division, Bhabha Atomic Research Centre",
"city": "Indore",
"country": "India",
"beamline_name": "Anton Paar SAXSpace",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "Chaperone protein DnaK",
"short_name": null,
"sequence": ">sp|P0A6Y8|DNAK_ECOLI Chaperone protein DnaK OS=Escherichia coli (strain K12) OX=83333 GN=dnaK PE=1 SV=2\r\nMGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVT\r\nNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVL\r\nKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYG\r\nLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLINYL\r\nVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKV\r\nTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKVAEFFGKE\r\nPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPT\r\nKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDA\r\nDGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGD\r\nHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLME\r\nIAQQQHAQQQTAGADASANNAKDDDVVDAEFEEVKDKK",
"organism": "Escherichia coli (strain K12)",
"uniprot_code": "P0A6Y8",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "unknown",
"molecular_type": "protein",
"uniprot_sequence": "MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVT\nNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVL\nKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYG\nLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLINYL\nVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKV\nTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKVAEFFGKE\nPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPT\nKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDA\nDGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGD\nHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLME\nIAQQQHAQQQTAGADASANNAKDDDVVDAEFEEVKDKK",
"mw": 69.114,
"total_mw": 69.114,
"number_molecules": 0,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Chaperone protein DnaK in complex with recombinant \"heme detoxification protein\" (HDP: Q8IL04)."
},
{
"long_name": "Heme ligase",
"short_name": "HDPpf",
"sequence": ">STR-6His-HDPpf\r\nMASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGSKNRFYYNLIIKRLYTRSGGLRKPQKVTNDPESINRKVYWCFEHKPVKRTIINLIYSHNELKIFSNLLNHPTVGSSLIHELSLDGPYTAFFPSNEAMQLINIESFNKLYNDENKLSEFVLNHVTKEYWLYRDLYGSSYQPWLMYNEKREAPEKLRNLLNNDLIVKIEGEFKHCNHSIYLNGSKIIRPNMKCHNGVVHIVDKPIIF",
"organism": "Plasmodium falciparum (isolate 3D7)",
"uniprot_code": "Q8IL04",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "unknown",
"molecular_type": "protein",
"uniprot_sequence": "MKNRFYYNLIIKRLYTRSGGLRKPQKVTNDPESINRKVYWCFEHKPVKRTIINLIYSHNE\nLKIFSNLLNHPTVGSSLIHELSLDGPYTAFFPSNEAMQLINIESFNKLYNDENKLSEFVL\nNHVTKEYWLYRDLYGSSYQPWLMYNEKREAPEKLRNLLNNDLIVKIEGEFKHCNHSIYLN\nGSKIIRPNMKCHNGVVHIVDKPIIF",
"mw": 28.132,
"total_mw": 28.132,
"number_molecules": 0,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Expression of recombinant HDPpf at 18°C resulted in minimal soluble protein. Co-expression with DnaK-DnaJ-GrpE (pKJE7) significantly improved solubility, but the protein did not bind to Ni-NTA resin. Downstream characterization confirmed that recombinant HDPpf is in complex with DnaK (DnaK-HDPpf)"
}
],
"buffer": {
"name": "20 mM Tris-Cl, 200 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Chaperone protein DnaK (E.coli) & recombinant Heme ligase (HDP) (P.fulciparum) protein complex",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Mumbai 400085, INDIA",
"full_name": "Bhabha Atomic Research Centre",
"webpage": null
}
],
"contributor_name": "Dr. Rahul",
"contributor_surname": "Singh",
"orcid": "https://orcid.org/0000-0003-4871-3600"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2019-02-26",
"storage_temperature": 4.0,
"cell_temperature": 25.0,
"exposure_time": 30.0,
"number_of_frames": 100,
"wavelength": 1.5406,
"sample_detector_distance": null,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.11,
"s_max": 4.0,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXF5_fit1_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "GASBOR 2.3i (r14885)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXF5_fit1_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/DnaK-HDP_6dBQCQj.fit",
"symmetry": "NA",
"comment": null,
"user": 649
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXF5_fit1_model2_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "AlphaFold 3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXF5_fit1_model2.pdb",
"model_mw": 82.37,
"bead_radius": null,
"log": null,
"symmetry": "NA",
"comment": "The PDB structure of DnaK (7KZI) is modeled with HDPpf (AlphaFold; Q8IL04) using the ab-initio Gasbo",
"user": 649
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXF5_fit1_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 35.33,
"p_value": 0.0,
"fit_residual_plot": "SASDXF5_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXF5_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/DnaK-HDP.log",
"software_version": "GASBOR 2.3i (r14885)",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXF5_fit2_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "AlphaFold 3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXF5_fit2_model1.pdb",
"model_mw": 82.37,
"bead_radius": null,
"log": null,
"symmetry": "NA",
"comment": "The PDB structure of DnaK (7KZI) is modeled with HDPpf (AlphaFold; Q8IL04) using the ab-initio Gasbo",
"user": 649
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXF5_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 48.441,
"p_value": 0.0,
"fit_residual_plot": "SASDXF5_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXF5_fit2.fit",
"fit_log": null,
"software_version": "ATSAS 3.3.0 (r14945)",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": null,
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 70.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 51.0,
"porod_mw_error": null,
"pddf_i0": 0.2824,
"pddf_i0_error": null,
"guinier_i0": 0.276735,
"guinier_i0_error": null,
"pddf_rg": 4.06,
"pddf_rg_error": null,
"guinier_rg": 3.828,
"guinier_rg_error": 0.108,
"pddf_dmax": 13.8,
"pddf_dmax_error": null,
"porod_volume": 83.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 8,
"guinier_point_last": 67,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDXF5_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-08-13T10:03:08.381002+02:00",
"bragg_peak": []
}
