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- SASDDV9: Mycobacterium tuberculosis DNA LigaseA with Nicked DNA -

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Basic information

Entry
Database: SASBDB / ID: SASDDV9
SampleMycobacterium tuberculosis DNA LigaseA with Nicked DNA
  • DNA ligase A (protein), Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
  • Nicked DNA (DNA)
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA ligation / peptidoglycan-based cell wall / DNA replication / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
DNA ligase-like, N-terminal NAD+-binding domain / 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 ...DNA ligase-like, N-terminal NAD+-binding domain / 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 (strain ATCC 25618 / H37Rv) (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 #2183
Type: dummy / Radius of dummy atoms: 4.00 A / Symmetry: P1 / Chi-square value: 0.724 / P-value: 0.752557
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Mycobacterium tuberculosis DNA LigaseA with Nicked DNA
Specimen concentration: 2.5 mg/ml / Entity id: 1197 / 1198
BufferName: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol / pH: 8
Entity #1197Type: protein / Description: DNA ligase A / Formula weight: 76.079 / Num. of mol.: 1
Source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
References: UniProt: P9WNV1
Sequence: VSSPDADQTA PEVLRQWQAL AEEVREHQFR YYVRDAPIIS DAEFDELLRR LEALEEQHPE LRTPDSPTQL VGGAGFATDF EPVDHLERML SLDNAFTADE LAAWAGRIHA EVGDAAHYLC ELKIDGVALS LVYREGRLTR ASTRGDGRTG EDVTLNARTI ADVPERLTPG ...Sequence:
VSSPDADQTA PEVLRQWQAL AEEVREHQFR YYVRDAPIIS DAEFDELLRR LEALEEQHPE LRTPDSPTQL VGGAGFATDF EPVDHLERML SLDNAFTADE LAAWAGRIHA EVGDAAHYLC ELKIDGVALS LVYREGRLTR ASTRGDGRTG EDVTLNARTI ADVPERLTPG DDYPVPEVLE VRGEVFFRLD DFQALNASLV EEGKAPFANP RNSAAGSLRQ KDPAVTARRR LRMICHGLGH VEGFRPATLH QAYLALRAWG LPVSEHTTLA TDLAGVRERI DYWGEHRHEV DHEIDGVVVK VDEVALQRRL GSTSRAPRWA IAYKYPPEEA QTKLLDIRVN VGRTGRITPF AFMTPVKVAG STVGQATLHN ASEIKRKGVL IGDTVVIRKA GDVIPEVLGP VVELRDGSER EFIMPTTCPE CGSPLAPEKE GDADIRCPNA RGCPGQLRER VFHVASRNGL DIEVLGYEAG VALLQAKVIA DEGELFALTE RDLLRTDLFR TKAGELSANG KRLLVNLDKA KAAPLWRVLV ALSIRHVGPT AARALATEFG SLDAIAAAST DQLAAVEGVG PTIAAAVTEW FAVDWHREIV DKWRAAGVRM VDERDESVPR TLAGLTIVVT GSLTGFSRDD AKEAIVARGG KAAGSVSKKT NYVVAGDSPG SKYDKAVELG VPILDEDGFR RLLADGPASR THHHHHH
Entity #1198Type: DNA / Description: Nicked DNA / Formula weight: 8.136 / Num. of mol.: 2
Sequence:
GGTAGATCAG TGTCTATGTA TGTCAG

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.081 Å / Dist. spec. to detc.: 1.1 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Mycobacterium tuberculosis DNA LigaseA with Nicked DNA
Measurement date: May 13, 2017 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /
MinMax
Q0.0309 4.9277
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 353 /
MinMax
Q0.0872881 1.74149
P(R) point1 353
R0 12.19
Result
Type of curve: single_conc /
ExperimentalPorod
MW121.04 kDa-
Volume-263.11 nm3

P(R)GuinierGuinier error
Forward scattering, I014.26 14.41 0.12
Radius of gyration, Rg4.355 nm4.36 nm0.05

MinMax
D-12.19
Guinier point13 58

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