SASDG65

Adenylation domain of DNA ligase A (LigA)

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2021-05-18T08:48:43.246132+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Adenylation domain of DNA ligase A (LigA)

Concentration— – 12.5 Buffer / pH50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol / 8.0
Experimental temperature10.0 Facility / beamlineCSIR-Central Drug Research Institute / Anton Paar SAXSpace
Wavelength0.154 nmExposure1800.0 s × 2

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
DNA ligase A
View sequence
MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPE
proteinMycobacterium tuberculosisP9WNV11–328monomerMolecule count 136.729 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1744[3]0.13146–4.8913 1/nmHas uncertainty columnMissing 00sasbdb/entries/65/sasdg65/source/SASDG65.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.88—nm
i0Guinier51634.0377.0arbitrary
i0P(r)50840.0—arbitrary
mwExperimental36.6—kDa
porod_volumePorod68.0—nm³
rgGuinier2.730.08nm
rgP(r)2.684—nm

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 2mM 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 date2019-05-21Storage / measurement temperature10.0 / 10.0
Exposure time1800.0Frames2
Wavelength0.154Sample-to-detector distance0.31
SourceX-ray in houseDetectorMythen2 R 1K
Facility / beamlineCSIR-Central Drug Research Institute / Anton Paar SAXSpace · Lucknow, India
q range0.131 – 4.891Sample 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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pddf:source record
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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:156 field values
Field pathRaw value
codeSASDG65
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleSalt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i> NAD <sup>+</sup> -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity
project.publication.titleSalt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i> NAD <sup>+</sup> -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity
project.publication.author_listAfsar M, Shukla A, Kumar N, Ramachandran R
project.publication.journalActa Crystallographica Section D Structural Biology
project.publication.doi10.1107/S2059798321003107
project.publication.pmidnull
project.publication.published_date2021 May 14
project.statusreleased
project.submitted_date2019-09-05
project.released_date2021-05-18
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intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDG65.dat
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experiment.instrument.detector.typeHybrid Photon Counting (HPC)
experiment.instrument.detector.nameMythen2 R 1K
experiment.instrument.detector.resolutionnull
experiment.instrument.nameCSIR-Central Drug Research Institute
experiment.instrument.cityLucknow
experiment.instrument.countryIndia
experiment.instrument.beamline_nameAnton Paar SAXSpace
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray in house
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_nameAdD
experiment.sample.molecule[0].sequenceMSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDF EPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTI ADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH VEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWA IAYKYPPE
experiment.sample.molecule[0].organismMycobacterium tuberculosis
experiment.sample.molecule[0].uniprot_codeP9WNV1
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last328
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].mw36.729
experiment.sample.molecule[0].total_mw36.729
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.buffer.name50 mM Tris-HCl 200 mM NaCl 2mM 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.nameAdenylation domain of DNA ligase A (LigA)
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.date2019-05-21
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time1800.0
experiment.number_of_frames2
experiment.wavelength0.154
experiment.sample_detector_distance0.31
experiment.concentration_minnull
experiment.concentration_max12.5
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.131
experiment.s_max4.891
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].softwareGASBOR
fits[0].chi_square_value0.02
fits[0].p_value0.008344
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fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of the adenylation domain of DNA ligase A in 50 mM Tris-HCl 200 mM NaCl 2 mM β-mercaptoethanol, pH 8 were collected using an Anton Paar SAXSpace at the CSIR-Central Drug Research Institute (Lucknow India) with a Mythen2 R 1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 12.50 mg/ml was measured at 10°C. Two successive 1800 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_unitarbitrary
experimental_mw36.6
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i050840.0
pddf_i0_errornull
guinier_i051634.0
guinier_i0_error377.0
pddf_rg2.684
pddf_rg_errornull
guinier_rg2.73
guinier_rg_error0.08
pddf_dmax8.88
pddf_dmax_errornull
porod_volume68.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first3
guinier_point_last55
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDG65_datloglog_img.png
symmetrynull
last_modified2021-05-18T08:48:43.246132+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDG65
statussuccess
started_at2026-08-11T16:36:37.301528+00:00
finished_at2026-08-11T16:36:45.143525+00:00
source_last_modified2021-05-18T08:48:43.246132+02:00
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View the complete summary.json source
{
  "code": "SASDG65",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i>\n              NAD <sup>+</sup>\n              -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity",
    "publication": {
      "title": "Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i>\n              NAD <sup>+</sup>\n              -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity",
      "author_list": "Afsar M, Shukla A, Kumar N, Ramachandran R",
      "journal": "Acta Crystallographica Section D Structural Biology",
      "doi": "10.1107/S2059798321003107",
      "pmid": null,
      "published_date": "2021 May 14"
    },
    "status": "released",
    "submitted_date": "2019-09-05",
    "released_date": "2021-05-18"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG65.out",
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        "resolution": null
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      "country": "India",
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      "type_of_source": "X-ray in house",
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    "sample": {
      "molecule": [
        {
          "long_name": "DNA ligase A",
          "short_name": "AdD",
          "sequence": "MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDF\r\nEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTI\r\nADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH\r\nVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWA\r\nIAYKYPPE",
          "organism": "Mycobacterium tuberculosis",
          "uniprot_code": "P9WNV1",
          "uniprot_range_first": 1,
          "uniprot_range_last": 328,
          "oligomerization": "monomer",
          "molecular_type": "protein",
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            "webpage": "https://cdri.res.in/"
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View the complete manifest.json source
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