{ "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": [], "intensity_unit": null, "experimental_mw": 127.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 127.0, "porod_mw_error": null, "pddf_i0": 87.79, "pddf_i0_error": null, "guinier_i0": 87.94, "guinier_i0_error": 0.13, "pddf_rg": 3.45, "pddf_rg_error": null, "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": [] }