Vaccinia virus binary E9 polymerase / DNA complex

{
  "code": "SASDCM5",
  "status": "Published",
  "type_of_curve": "Other",
  "angular_unit": "1/nm",
  "project": {
    "title": "The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.",
    "publication": {
      "title": "The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.",
      "author_list": "Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-017-01542-z",
      "pmid": "29129932",
      "published_date": "2017 Nov 13"
    },
    "status": "released",
    "submitted_date": "2017-06-27",
    "released_date": "2017-11-20"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCM5.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCM5.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM5_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM5_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCM5_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM5_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCM5.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": "DNA polymerase E9 exo- mutant",
          "short_name": "E9 exo-",
          "sequence": "GAMDPDVRCINWFESHGENRFLYLKSRCRNGETVFIRFPHYFYYVVTDEIYQSLSPPPFNARPLGKMRTIDIDETIS\r\nYNLDIKDRKCSVADMWLIEEPKKRSIQNATMDEFLNISWFYISNGISPDGCYSLDEQYLTKINNGCYHCDDPRNCFAKKI\r\nPRFDIPRSYLFLAIACHFDKKFPSVFINPISHTSYCYIDLSGKRLLFTLINEEMLTEQEIQEAVDRGCLRIQSLMEMDYE\r\nRELVLCSEIVLLRIAKQLLELTFDYVVTFNGHNFDLRYITNRLELLTGEKIIFRSPDKKEAVHLCIYERNQSSHKGVGGM\r\nANTTFHVNNNNGTIFFDLYSFIQKSEKLDSYKLDSISKNAFSCMGKVLNRGVREMTFIGDDTTDAKGKAAAFAKVLTTGN\r\nYVTVDEDIICKVIRKDIWENGFKVVLLCPTLPNDTYKLSFGKDDVDLAQMYKDYNLNIALDMARYCIHDACLCQYLWEYY\r\nGVETKTDAGASTYVLPQSMVFEYRASTVIKGPLLKLLLETKTILVRSETKQKFPYEGGKVFAPKQKMFSNNVLIFDYNSL\r\nYPNVCIFGNLSPETLVGVVVSTNRLEEEINNQLLLQKYPPPRYITVHCEPRLPNLISEIAIFDRSIEGTIPRLLRTFLAE\r\nRARYKKMLKQATSSTEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYLESVLNGAELSNGMLR\r\nFANPLSNPFYMDDRDINPIVKTSLPIDYRFRFRSVYGDTDSVFTEIDSQDVDKSIEIAKELERLINNRVLFNNFKIEFEA\r\nVYKNLIMQSKKKYTTMKYSASSNSKSVPERINKGTSETRRDVSKFHKNMIKTYKTRLSEMLSEGRMNSNQVCIDILRSLE\r\nTDLRSEFDSRSSPLELFMLSRMHHSNYKSADNPNMYLVTEYNKNNPETIELGERYYFAYICPANVPWTKKLVNIKTYETI\r\nIDRSFKLGSDQRIFYEVYFKRLTSEIVNLLDNKVLCISFFERMFGSKPTFYEA",
          "organism": "Vaccinia virus",
          "uniprot_code": "P20509",
          "uniprot_range_first": 1,
          "uniprot_range_last": 1006,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MDVRCINWFESHGENRFLYLKSRCRNGETVFIRFPHYFYYVVTDEIYQSLSPPPFNARPL\nGKMRTIDIDETISYNLDIKDRKCSVADMWLIEEPKKRSIQNATMDEFLNISWFYISNGIS\nPDGCYSLDEQYLTKINNGCYHCDDPRNCFAKKIPRFDIPRSYLFLDIECHFDKKFPSVFI\nNPISHTSYCYIDLSGKRLLFTLINEEMLTEQEIQEAVDRGCLRIQSLMEMDYERELVLCS\nEIVLLRIAKQLLELTFDYVVTFNGHNFDLRYITNRLELLTGEKIIFRSPDKKEAVHLCIY\nERNQSSHKGVGGMANTTFHVNNNNGTIFFDLYSFIQKSEKLDSYKLDSISKNAFSCMGKV\nLNRGVREMTFIGDDTTDAKGKAAAFAKVLTTGNYVTVDEDIICKVIRKDIWENGFKVVLL\nCPTLPNDTYKLSFGKDDVDLAQMYKDYNLNIALDMARYCIHDACLCQYLWEYYGVETKTD\nAGASTYVLPQSMVFEYRASTVIKGPLLKLLLETKTILVRSETKQKFPYEGGKVFAPKQKM\nFSNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVSTNRLEEEINNQLLLQKYPPPRYITVH\nCEPRLPNLISEIAIFDRSIEGTIPRLLRTFLAERARYKKMLKQATSSTEKAIYDSMQYTY\nKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYLESVLNGAELSNGMLRFANPLSN\nPFYMDDRDINPIVKTSLPIDYRFRFRSVYGDTDSVFTEIDSQDVDKSIEIAKELERLINN\nRVLFNNFKIEFEAVYKNLIMQSKKKYTTMKYSASSNSKSVPERINKGTSETRRDVSKFHK\nNMIKTYKTRLSEMLSEGRMNSNQVCIDILRSLETDLRSEFDSRSSPLELFMLSRMHHSNY\nKSADNPNMYLVTEYNKNNPETIELGERYYFAYICPANVPWTKKLVNIKTYETIIDRSFKL\nGSDQRIFYEVYFKRLTSEIVNLLDNKVLCISFFERMFGSKPTFYEA",
          "mw": 117.14,
          "total_mw": 117.14,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "DNA oligomer template-primer hairpin",
          "short_name": "DNA hairpin",
          "sequence": "AAAGGCGCTGCTGAGTTTTCTCAGCAGCG",
          "organism": "synthetic construct",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "DNA",
          "uniprot_sequence": null,
          "mw": 9.014,
          "total_mw": 9.014,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris HCl, 100 mM NaCl, 4 mM DTT",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Vaccinia virus binary E9 polymerase /  DNA complex",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "IBS",
            "address": "Grenoble, France",
            "full_name": "Institut de Biologie Structurale",
            "webpage": ""
          }
        ],
        "contributor_name": "Wim",
        "contributor_surname": "Burmeister",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-03-12",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 700,
    "wavelength": 0.0992,
    "sample_detector_distance": 2.864,
    "concentration_min": null,
    "concentration_max": null,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.043,
    "s_max": 4.975,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCM5_fit1_model1_img.png",
          "software": "PyMOL",
          "pdb_link": [
            {
              "pdb_code": "5n2h",
              "ext_code": "5N2H",
              "ext_type": "pdb",
              "difference_with_model": "derived"
            }
          ],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": "",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCM5_fit1_model1.pdb",
          "model_mw": 124.7,
          "bead_radius": 1.9,
          "log": "https://www.sasbdb.org/media/log_files/closed_e9_DNA.log",
          "symmetry": "none",
          "comment": "DNA and conformation from entry 3iay, domainwise alignment of E9 structure",
          "user": 226
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCM5_fit1_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 1.08,
      "p_value": 0.00012,
      "fit_residual_plot": null,
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCM5_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/closed_e9_DNA.log",
      "software_version": "2.8.3",
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Binary E9 polymerase / DNA complex in 20 mM Tris HCl, 100 mM NaCl, 4 mM DTT, pH 7 were collected using size exclusion chromatography coupled SAXS (SEC-SAXS) 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 = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Data were collected at at 20°C during the course of elution (700 successive 1 second frames). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the resulting subtracted curves were scaled and averaged.",
  "tags": [],
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  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
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  "porod_mw_error": null,
  "pddf_i0": 87.79,
  "pddf_i0_error": null,
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  "guinier_i0_error": 0.13,
  "pddf_rg": 3.45,
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  "guinier_rg": 3.47,
  "guinier_rg_error": 0.02,
  "pddf_dmax": 12.0,
  "pddf_dmax_error": null,
  "porod_volume": 210.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 13,
  "guinier_point_last": 66,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDCM5_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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