{ "code": "SASDDH6", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.", "publication": { "title": "Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.", "author_list": "Thongkawphueak T, Winter AJ, Williams C, Maple HJ, Soontaranon S, Kaewhan C, Campopiano DJ, Crump MP, Wattana-Amorn P", "journal": "Biochemistry", "doi": "10.1021/acs.biochem.0c00830", "pmid": "33416314", "published_date": "2021 Jan 8" }, "status": "released", "submitted_date": "2018-05-10", "released_date": "2020-03-25" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDH6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDH6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDH6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDH6.sascif", "experiment": { "instrument": { "detector": { "type": "CCD", "name": "Rayonix SX165", "resolution": 15.0 }, "name": "Synchrotron Light Research Institute (SLRI)", "city": "Nakhon Ratchasima", "country": "Thailand", "beamline_name": "BL1.3W", "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": "Di-domain acyl carrier protein of PigH from prodigiosin biosynthesis", "short_name": "Di-domain ACP", "sequence": ">PigHACP1ACP2\r\nGSHMNDVTTETYETLKQSVLHTFAQLTGYNVSELSLTSHLENDLGVDSIALAEIAVSLSRQFQLNTPLLIQDINTIKDALDGILQREFQLSEKVEPAAIALSGDADLWLGNLVRQIFASHSGYDVNALALDAEIESDLGIDSVSVASAQGELFNTLQLNSETIIANCNTLSALKQCLAARLVQEKGQDWFELTRAPPPPPLRSGC", "organism": "Serratia sp. ATCC 39006", "uniprot_code": "Q5W264", "uniprot_range_first": 4, "uniprot_range_last": 191, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MNDVTTETYETLKQSVLHTFAQLTGYNVSELSLTSHLENDLGVDSIALAEIAVSLSRQFQ\nLNTPLLIQDINTIKDALDGILQREFQLSEKVEPAAIALSGDADLWLGNLVRQIFASHSGY\nDVNALALDAEIESDLGIDSVSVASAQGELFNTLQLNSETIIANCNTLSALKQCLAARLVQ\nEKGQDWFEQRGRGQSDSAIDHDADTTAEVTPPTATPVAINAEIGDPRTMRDFVGIEHPDI\nFHKAREFHLFYQDKKKRQLYFYGMPLETPCKNRAVMFDEATGQHREFLMFGSNSYLGLSN\nHPEIIHAIQDAASLYGATNTGCRIIAGSNVLHLELERKLAKLKGRDDCIVYPSGYSANLG\nCISALTSRHDLVFTDAINHMSIQDGCKLAGAQRKIYNHSLTSLEKSLAKYADHPGGKLIV\nTDGVFSMHGDIVDLPRLMKLAERYGARVLVDDAHSTGVLGKTGAGTSEHFNMKGQVDLEL\nGTMSKALSGLGGYVCGDGDVVEYLRFYSNSYVFAATIPAPVAAGVIASIDVMLREPERLA\nKLWDNIYYFRTRLLNAGFDLENSDSAIIPIVVGDDAKTLFFGRAVRARGMFCQTVVFPGV\nSVGDARLRISITSEHTREDLDEAYAILVASALEVGVPVNASAHQEENASVAEA", "mw": 22.209, "total_mw": 22.209, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris supplemented with 5 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Di-domain acyl carrier protein of the seryltransferase from prodigiosin biosynthesis", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Thailand", "full_name": "Kasetsart University", "webpage": "https://www.ku.ac.th" } ], "contributor_name": "Pakorn", "contributor_surname": "Wattana-Amorn", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-01-13", "storage_temperature": 25.0, "cell_temperature": 25.0, "exposure_time": 600.0, "number_of_frames": 1, "wavelength": 0.131, "sample_detector_distance": 0.85, "concentration_min": 1.7, "concentration_max": 6.8, "sample_volume": null, "flow_rate": null, "s_min": 0.411, "s_max": 3.612, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDH6_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r6669", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDH6_fit1_model1.pdb", "model_mw": 22.5, "bead_radius": 1.8, "log": null, "symmetry": "P1", "comment": null, "user": 318 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDH6_fit1_model2_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDH6_fit1_model2.pdb", "model_mw": 22.461, "bead_radius": 2.0, "log": null, "symmetry": null, "comment": null, "user": 318 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDH6_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 2.864, "p_value": 0.3102, "fit_residual_plot": "SASDDH6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH6_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run_1_alDHk3F.log", "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.5a", "i0_calibration_standard": null, "description": "Two DAMMIF-derived dummy atom models are displayed. Top: The best-fit individual DAMMIF model and corresponding fit to the SAXS data. Bottom: The average spatial representation of the protein obtained after the alignment of multiple individual DAMMIF models combined with volume and bead-occupancy corrections (damfilt).", "experiment_description": "Synchrotron SAXS data from solutions of the di-domain acyl carrier protein of the seryltransferase from prodigiosin biosynthesis in 20 mM Tris, 5 mM DTT, pH 7, were collected on the BL1.3W beam line at the Synchrotron Light Research Institute (Nakhon Ratchasima, Thailand) using a CCD Rayonix SX165 detector at a sample-detector distance of 0.9 m and at a wavelength of λ = 0.131 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.7 and 6.8 mg/ml were measured at 25°C. One 600 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. 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": [], "intensity_unit": "arbitrary", "experimental_mw": 19.107, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 2.343e-05, "pddf_i0_error": 3.811e-06, "guinier_i0": 2.2764e-05, "guinier_i0_error": 1.6e-06, "pddf_rg": 2.56, "pddf_rg_error": 0.36, "guinier_rg": 2.39, "guinier_rg_error": 0.18, "pddf_dmax": 8.43, "pddf_dmax_error": null, "porod_volume": 39.44, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 11, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDH6_datloglog_img.png", "symmetry": null, "last_modified": "2024-10-17T15:41:17.447524+02:00", "bragg_peak": [] }