GppNHp bound form of C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GppNHp)

{
  "code": "SASDBV6",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Structural and biochemical analysis of <i>Escherichia coli</i> ObgE, a central regulator of bacterial persistence.",
    "publication": {
      "title": "Structural and biochemical analysis of <i>Escherichia coli</i> ObgE, a central regulator of bacterial persistence.",
      "author_list": "Gkekas S, Singh RK, Shkumatov AV, Messens J, Fauvart M, Verstraeten N, Michiels J, Versées W",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.M116.761809",
      "pmid": "28223358",
      "published_date": "2017 Apr 7"
    },
    "status": "released",
    "submitted_date": "2016-09-28",
    "released_date": "2017-02-23"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBV6.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBV6.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBV6_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBV6_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBV6_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBV6_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBV6.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "CCD",
        "name": "AVIEX PCCD170170",
        "resolution": null
      },
      "name": "SOLEIL",
      "city": "Saint-Aubin",
      "country": "France",
      "beamline_name": "SWING",
      "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": "GTPase ObgE/CgtA",
          "short_name": "ObgE_340",
          "sequence": "MGSSHHHHHHSSGLVPRGSHMKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYR\r\nFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKGGWHGLGNTRFKSSVNRTPRQ\r\nKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVSAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEG\r\nAAEGAGLGIRFLKHLERCRVLLHLIDIDPIDGTDPVENARIIISELELYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI\r\nAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVA",
          "organism": "Escherichia coli",
          "uniprot_code": "P42641",
          "uniprot_range_first": 1,
          "uniprot_range_last": 340,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYR\nFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKG\nGWHGLGNTRFKSSVNRTPRQKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVS\nAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRV\nLLHLIDIDPIDGTDPVENARIIISELEKYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI\nAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVVQAEEAKQPEKVEFMWDDYHRQQ\nLEEIAEEDDEDWDDDWDEDDEEGVEFIYKR",
          "mw": 38.899,
          "total_mw": 38.899,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Hepes, 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT, 400 µM GppNHp",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "GppNHp bound form of C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GppNHp)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "VUB",
            "address": "Pleinlaan 2 1050 Brussel ",
            "full_name": "Vrije Universiteit Brussel",
            "webpage": "http://www.vub.ac.be/"
          }
        ],
        "contributor_name": "Alexander",
        "contributor_surname": "Shkumatov",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-03-12",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 2.8,
    "number_of_frames": 255,
    "wavelength": 0.103,
    "sample_detector_distance": 1.79,
    "concentration_min": 7.0,
    "concentration_max": null,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.062,
    "s_max": 6.142,
    "total_exposure_time": null,
    "seccolumn": null
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  "fits": [
    {
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBV6_fit1_model1_img.png",
          "software": "DAMMIN",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": "r7897M",
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          "model_mw": 34.2,
          "bead_radius": 2.75,
          "log": "https://www.sasbdb.org/media/log_files/refine_NwPTf53.log",
          "symmetry": "P1",
          "comment": "",
          "user": 104
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBV6_fit1_fit_img.png",
      "software": null,
      "chi_square_value": 6.78,
      "p_value": 0.600511,
      "fit_residual_plot": "SASDBV6_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBV6_fit1.fir",
      "fit_log": null,
      "software_version": null,
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "G N O M   4.6",
  "i0_calibration_standard": null,
  "description": "The sample protein includes an N-terminal poly-histidine tag; frames corresponding to the peak in HPLC-SAXS run were averaged using DATAVER v0.2 (r3709)",
  "experiment_description": "Synchrotron SAXS data from solutions of the GppNHp bound form of the C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GppNHp) in 20 mM HEPES, 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT, 400 µM GppNHp, pH 7.5, were collected at the SWING beam line at the SOLEIL Synchrotron (Saint-Aubin, France) using a CCD AVIEX detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Data collection was performed at at 10°C. 255 successive 2.8 second frames were collected through an HPLC-SEC elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration, then averaged to produce the final SAXS profile displayed in this entry.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 44.8,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 42.0,
  "porod_mw_error": null,
  "pddf_i0": 0.03857,
  "pddf_i0_error": 1.2e-05,
  "guinier_i0": 0.038495,
  "guinier_i0_error": 2.1e-05,
  "pddf_rg": 3.18,
  "pddf_rg_error": 0.002,
  "guinier_rg": 3.11,
  "guinier_rg_error": 0.04,
  "pddf_dmax": 11.4,
  "pddf_dmax_error": 1.0,
  "porod_volume": 72.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 18,
  "guinier_point_last": 46,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBV6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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