{ "code": "SASDG43", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "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/SASDG43.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG43.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG43_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG43_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG43_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG43_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG43.sascif", "experiment": { "instrument": { "detector": { "type": "SANS", "name": "6Li-Scintillator 1 mm thickness + photomultiplier", "resolution": 5.3 }, "name": "FRM2", "city": "Munich", "country": "Germany", "beamline_name": "KWS1", "beam_geometry": null, "type_of_source": "neutron source", "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 42%D2O", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.6, "deuteration": null }, "purity_method": null, "name": "The Pyrococcus furiosus Box C/D sRNP complex reconstituted with 1H Nop5, 1H L7Ae, 1H st-sR26 RNA, 1H substrate D and 2H Fibrillarin (SANS data in 42% v/v D2O)", "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": "2015-05-24", "storage_temperature": 24.0, "cell_temperature": 55.0, "exposure_time": 7200.0, "number_of_frames": 1, "wavelength": 0.5, "sample_detector_distance": 4.0, "concentration_min": null, "concentration_max": 7.7, "sample_volume": null, "flow_rate": null, "s_min": 0.125, "s_max": 1.437, "total_exposure_time": null, "seccolumn": null }, "fits": [], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.5a", "i0_calibration_standard": null, "description": null, "experiment_description": "SANS data from solutions of the Pyrococcus furiosus Box C/D sRNP complex reconstituted with 1H Nop5, 1H L7Ae, 1H st-sR26 RNA, 1H substrate D and 2H Fibrillarin in 50 mM phosphate 500 mM NaCl 42%D2O, pH 6.6 were collected on KWS1 (FRM2; Munich, Germany) using a 6Li-Scintillator 1 mm thickness + photomultiplier detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.5 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 7.70 mg/ml was measured at 55°C. One 7200 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.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 200.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.4772, "pddf_i0_error": null, "guinier_i0": 0.46, "guinier_i0_error": 0.0089, "pddf_rg": 5.38, "pddf_rg_error": null, "guinier_rg": 4.938, "guinier_rg_error": 0.418, "pddf_dmax": 16.6, "pddf_dmax_error": null, "porod_volume": 65.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 6, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDG43_datloglog_img.png", "symmetry": null, "last_modified": "2020-03-25T10:03:55.945676+01:00", "bragg_peak": [] }