SASDDV9

Mycobacterium tuberculosis DNA LigaseA with Nicked DNA

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2020-10-01T10:29:14.179535+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Mycobacterium tuberculosis DNA LigaseA with Nicked DNA

Concentration— – 2.5 Buffer / pH50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol / 8.0
Experimental temperature10.0 Facility / beamlineESRF / BM29
Wavelength0.081 nmExposure1.0 s × 10

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
DNA ligase A
View sequence
VSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRTHHHHHH
proteinMycobacterium tuberculosisP9WNV1—–—monomerMolecule count 176.079 kDa
Nicked DNA
View sequence
GGTAGATCAGTGTCTATGTATGTCAG
DNA———–—dimerMolecule count 28.136 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11043[3]0.03089495–4.927699 1/nmHas uncertainty columnMissing 029sasbdb/entries/v9/sasddv9/source/SASDDV9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)14.79—nm
i0Guinier14.410.12—
i0P(r)14.50.13—
mwExperimental121.04—kDa
porod_volumePorod262.0—nm³
rgGuinier4.360.05nm
rgP(r)4.4990.07nm

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

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3. Source Fits and Models Source Fits & Models

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4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

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6. Complete Source Record Complete Source Record

The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer name50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanolBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-05-13Storage / measurement temperature10.0 / 10.0
Exposure time1.0Frames10
Wavelength0.081Sample-to-detector distance1.1
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.031 – 4.928Sample volume / flow rate— / —

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:173 field values
Field pathRaw value
codeSASDDV9
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleM. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.
project.publication.titleM. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.
project.publication.author_listKhanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gkaa188
project.publication.pmid32232338
project.publication.published_date2020 Mar 30
project.statusreleased
project.submitted_date2018-09-06
project.released_date2019-05-28
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDDV9.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDDV9.dat
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intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDV9_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDDV9.sascif
experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameDNA ligase A
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceVSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRTHHHHHH
experiment.sample.molecule[0].organismMycobacterium tuberculosis
experiment.sample.molecule[0].uniprot_codeP9WNV1
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE LRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC ELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE VRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH VEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK VDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG STVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE CGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA DEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT AARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM VDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG SKYDKAVELGVPILDEDGFRRLLADGPASRT
experiment.sample.molecule[0].mw76.079
experiment.sample.molecule[0].total_mw76.079
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.molecule[1].long_nameNicked DNA
experiment.sample.molecule[1].short_namenull
experiment.sample.molecule[1].sequenceGGTAGATCAGTGTCTATGTATGTCAG
experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeDNA
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw8.136
experiment.sample.molecule[1].total_mw16.272
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameMycobacterium tuberculosis DNA LigaseA with Nicked DNA
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressIndia
experiment.contributor[0].affiliation[0].full_nameCSIR - Central Drug Research Institute
experiment.contributor[0].affiliation[0].webpagehttps://cdri.res.in/
experiment.contributor[0].contributor_nameRavishankar
experiment.contributor[0].contributor_surnameRamachandran
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-05-13
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.081
experiment.sample_detector_distance1.1
experiment.concentration_minnull
experiment.concentration_max2.5
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.031
experiment.s_max4.928
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMFILT
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].model_mwnull
fits[0].models[0].bead_radius4.0
fits[0].models[0].lognull
fits[0].models[0].symmetryP1
fits[0].models[0].commentnull
fits[0].models[0].user328
fits[0].fit_unit1/A
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fits[0].softwareDAMMIF
fits[0].chi_square_value1.702
fits[0].p_value0.7614
fits[0].fit_residual_plotSASDDV9_fit1_fitresiduals_img.png
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fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Mycobacterium tuberculosis DNA LigaseA with nicked DNA in 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol, pH 8 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 1.1 m and at a wavelength of λ = 0.081 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.50 mg/ml was measured at 10°C. 10 successive 1 second frames were 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_unitnull
experimental_mw121.04
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i014.5
pddf_i0_error0.13
guinier_i014.41
guinier_i0_error0.12
pddf_rg4.499
pddf_rg_error0.07
guinier_rg4.36
guinier_rg_error0.05
pddf_dmax14.79
pddf_dmax_errornull
porod_volume262.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first13
guinier_point_last58
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDDV9_datloglog_img.png
symmetrynull
last_modified2020-10-01T10:29:14.179535+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDDV9
statussuccess
started_at2026-08-11T16:39:05.885573+00:00
finished_at2026-08-11T16:39:14.351340+00:00
source_last_modified2020-10-01T10:29:14.179535+02:00
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View the complete summary.json source
{
  "code": "SASDDV9",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.",
    "publication": {
      "title": "M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.",
      "author_list": "Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkaa188",
      "pmid": "32232338",
      "published_date": "2020 Mar 30"
    },
    "status": "released",
    "submitted_date": "2018-09-06",
    "released_date": "2019-05-28"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDV9.out",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDV9.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
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      "sample_path_length": null,
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          "organism": "Mycobacterium tuberculosis",
          "uniprot_code": "P9WNV1",
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          "deuteration": null,
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        "affiliation": [
          {
            "short_name": null,
            "address": "India",
            "full_name": "CSIR - Central Drug Research Institute",
            "webpage": "https://cdri.res.in/"
          }
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        "contributor_name": "Ravishankar",
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  "last_modified": "2020-10-01T10:29:14.179535+02:00",
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View the complete manifest.json source
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