{ "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": [] }