The Pyrococcus furiosus Box C/D sRNP complex reconstituted with 1H Nop5, 1H L7Ae, 1H st-sR26 RNA, 1H substrate D and 2H Nop5 (SANS data in 42% v/v D2O)

{
  "code": "SASDG53",
  "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/SASDG53.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG53.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG53_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG53_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG53_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG53_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG53.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "128 linear sensitive multidetector",
        "name": "Reuter-Stokes 3He",
        "resolution": 0.8
      },
      "name": "Institut Laue-Langevin (ILL)",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "D22",
      "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 Nop5 (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": "2015-09-21",
    "storage_temperature": 24.0,
    "cell_temperature": 55.0,
    "exposure_time": 900.0,
    "number_of_frames": 1,
    "wavelength": 0.6,
    "sample_detector_distance": 4.0,
    "concentration_min": null,
    "concentration_max": 5.4,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.128,
    "s_max": 2.388,
    "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": "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 Nop5 in 50 mM phosphate 500 mM NaCl 42%D2O, pH 6.6 were collected on D22 (ILL; Grenoble, France) using a 128 linear sensitive Reuter-Stokes detector detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.6 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.40 mg/ml was measured at 55°C. One 900 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",
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  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 0.3353,
  "pddf_i0_error": null,
  "guinier_i0": 0.338,
  "guinier_i0_error": 0.0017,
  "pddf_rg": 4.1,
  "pddf_rg_error": null,
  "guinier_rg": 4.125,
  "guinier_rg_error": 0.068,
  "pddf_dmax": 14.0,
  "pddf_dmax_error": null,
  "porod_volume": 222.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 9,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDG53_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2022-08-15T14:51:04.900446+02:00",
  "bragg_peak": []
}

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