{ "code": "SASDGA3", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "The guide sRNA sequence determines the activity level of box C/D RNPs.", "publication": { "title": "The guide sRNA sequence determines the activity level of box C/D RNPs.", "author_list": "Graziadei A, Gabel F, Kirkpatrick J, Carlomagno T", "journal": "Elife", "doi": "10.7554/eLife.50027", "pmid": "32202498", "published_date": "2020 Mar 23" }, "status": "released", "submitted_date": "2019-07-29", "released_date": "2020-03-25" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGA3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGA3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGA3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGA3.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "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, "xray_energy": null, "beam_profile_ah": null, "beam_profile_al": null }, "sample": { "molecule": [ { "long_name": "Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase", "short_name": "Fibrillarin", "sequence": ">sp|Q8U4M2|FLPA_PYRFU Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=flpA PE=1 SV=1\r\nMVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGA\r\nAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEE\r\nRRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKS\r\nRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP", "organism": "Pyrococcus furiosus", "uniprot_code": "Q8U4M2", "uniprot_range_first": 1, "uniprot_range_last": 227, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGA\nAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEE\nRRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKS\nRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP", "mw": 25.761, "total_mw": 51.522, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "50S ribosomal protein L7Ae", "short_name": "L7Ae", "sequence": ">sp|Q8U160|RL7A_PYRFU 50S ribosomal protein L7Ae OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=rpl7ae PE=1 SV=2\r\nMAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPE\r\nEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKE\r\nLMK", "organism": "Pyrococcus furiosus", "uniprot_code": "Q8U160", "uniprot_range_first": 1, "uniprot_range_last": 123, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPE\nEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKE\nLMK", "mw": 13.395, "total_mw": 26.79, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "NOP5/NOP56 related protein", "short_name": "Nop5", "sequence": ">tr|Q8U4M1|Q8U4M1_PYRFU NOP5/NOP56 related protein OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=PF0060 PE=1 SV=1\r\nMKAFISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYD\r\nEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRI\r\nQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTV\r\nGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKK\r\nLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLR\r\nTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEA\r\nRIREIKEKYPKPPKRKREERKGKKPWKKDKKKKKKKEKPRRR", "organism": "Pyrococcus furiosus", "uniprot_code": "Q8U4M1", "uniprot_range_first": 1, "uniprot_range_last": 402, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MKAFISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYD\nEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRI\nQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTV\nGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKK\nLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLR\nTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEA\nRIREIKEKYPKPPKRKREERKGKKPWKKDKKKKKKKEKPRRR", "mw": 46.788, "total_mw": 93.576, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "pyrococcus furiosus sR26 stabilized construct", "short_name": "st-sR26", "sequence": ">st-sR26\r\nGCGAGCAAUGAUGAGUGAUGGGCGAACUGAGCUCGAAAGAGCAAUGAUGACGGAGGUGAUCACUGAGCUCGC", "organism": "Pyrococcus furiosus", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": null, "mw": 23.548, "total_mw": 23.548, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Pyrococcus furiosus sR26 substrate D", "short_name": "Substrate D", "sequence": ">Substrate D\r\nGUAGAUCACCUCCG", "organism": "Pyrococcus furiosus", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": null, "mw": 4.486, "total_mw": 4.486, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM phosphate 500 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.6, "deuteration": null }, "purity_method": null, "name": "Pyrococcus furiosus Box C/D sRNP reconstituted with st-sR6 sRNA bound to substrate D (SAXS data)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Germany", "full_name": "Leibniz University of Hannover", "webpage": "https://www.uni-hannover.de" } ], "contributor_name": "Andrea", "contributor_surname": "Graziadei", "orcid": "https://orcid.org/0000-0001-7709-6002" } ], "concentration_method": null, "concentration_unit": null, "date": "2015-07-13", "storage_temperature": 20.0, "cell_temperature": 40.1, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.09919, "sample_detector_distance": 2.864, "concentration_min": null, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.033, "s_max": 4.934, "total_exposure_time": null, "seccolumn": null }, "fits": [], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Pyrococcus furiosus Box C/D sRNP reconstituted with st-sR6 sRNA bound to substrate D in 50 mM phosphate 500 mM NaCl, pH 6.6 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 40.1°C. 10 successive 1 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": "arbitrary", "experimental_mw": 214.0, "experimental_mw_error": null, "guinier_i0_mw": 214.9, "guinier_i0_mw_error": 0.1, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 214.5, "pddf_i0_error": null, "guinier_i0": 214.87, "guinier_i0_error": 0.1, "pddf_rg": 5.0, "pddf_rg_error": null, "guinier_rg": 5.0, "guinier_rg_error": 0.01, "pddf_dmax": 17.0, "pddf_dmax_error": null, "porod_volume": 429.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 16, "guinier_point_last": 49, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDGA3_datloglog_img.png", "symmetry": null, "last_modified": "2020-03-25T10:04:13.882830+01:00", "bragg_peak": [] }