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- SASDD88: The BRCT domain from Mycobacterium tuberculosis DNA ligase -

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Basic information

Entry
Database: SASBDB / ID: SASDD88
SampleThe BRCT domain from Mycobacterium tuberculosis DNA ligase
  • M.tb. LigA BRCT domain (DNA ligase A) (protein), BRCT, Mycobacterium tuberculosis
Function / homology
Function and homology information


base-excision repair, DNA ligation / DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA ligation / peptidoglycan-based cell wall / DNA replication / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal ...Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
Contact author
  • Ravishankar Ramachandran (CSIR-Central Drug Research Institute)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2056
Type: dummy / Radius of dummy atoms: 1.30 A / Symmetry: P1 / Chi-square value: 0.785 / P-value: 0.000494
Search similar-shape structures of this assembly by Omokage search (details)
Model #2058
Type: atomic / Symmetry: P1 / Chi-square value: 4.49835837712976
Search similar-shape structures of this assembly by Omokage search (details)
Model #2091
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 2.79002473758130
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: The BRCT domain from Mycobacterium tuberculosis DNA ligase
Specimen concentration: 10 mg/ml
BufferName: 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol / pH: 8
Entity #1092Name: BRCT / Type: protein / Description: M.tb. LigA BRCT domain (DNA ligase A) / Formula weight: 9.449 / Num. of mol.: 1 / Source: Mycobacterium tuberculosis / References: UniProt: P9WNV1
Sequence:
VDERDESVPR TLAGLTIVVT GSLTGFSRDD AKEAIVARGG KAAGSVSKKT NYVVAGDSPG SKYDKAVELG VPILDEDGFR RLLADGPASR T

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Experimental information

BeamInstrument name: CSIR-Central Drug Research Institute Anton Paar SAXSpace
City: Lucknow / 国: India / Type of source: X-ray in house / Wavelength: 0.154 Å / Dist. spec. to detc.: 0.3171 mm
DetectorName: Mythen2 R 1K / Type: Hybrid Photon Counting (HPC)
Scan
Title: The BRCT domain from Mycobacterium tuberculosis DNA ligase
Measurement date: Jun 2, 2018 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1800 sec. / Number of frames: 2 / Unit: 1/nm /
MinMax
Q0.0908 7.3679
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1055 /
MinMax
Q0.090776 6.82769
P(R) point1 1055
R0 3.73
Result
Type of curve: single_conc
Comments: The experimental molecular weight quoted for this entry was evaluated using calibrated size-exclusion chromatography (GE Healthcare Superdex75 10/30 column). The atomistic models displayed ...Comments: The experimental molecular weight quoted for this entry was evaluated using calibrated size-exclusion chromatography (GE Healthcare Superdex75 10/30 column). The atomistic models displayed in this entry (ribbon format) are a parent Phyre2 protein homology model (top) and one of ten structures obtained from the parent after elNémo normal mode calculations (bottom). Refer to: Kelley et al. (2015) Nature Protocols 10, 845-858; Suhre & Sanejouand (2004) Nucleic Acids Res. 32(Web Server issue): W610–W614.
ExperimentalPorod
MW15.3 kDa-
Volume-22.59 nm3

P(R)GuinierGuinier error
Forward scattering, I024290 25148.2 58.86
Radius of gyration, Rg1.441 nm1.58 nm0.02

MinMax
D-3.73
Guinier point1 115

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