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- SASDEW3: DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III pr... -

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Basic information

Entry
Database: SASBDB / ID: SASDEW3
SampleDNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA)
  • DNA ligase A (protein), MtbLigA, Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
  • Probable exodeoxyribonuclease III protein XthA (protein), MtbXthA, Mycobacterium tuberculosis
Function / homology
Function and homology information


: / DNA ligase (NAD+) / DNA ligase (NAD+) activity / exodeoxyribonuclease III / peptidoglycan-based cell wall / endonuclease activity / DNA replication / DNA repair / magnesium ion binding / DNA binding ...: / DNA ligase (NAD+) / DNA ligase (NAD+) activity / exodeoxyribonuclease III / peptidoglycan-based cell wall / endonuclease activity / DNA replication / DNA repair / magnesium ion binding / DNA binding / plasma membrane / cytosol
Similarity search - Function
Exodeoxyribonuclease III-like / 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 ...Exodeoxyribonuclease III-like / 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 / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / RuvA domain 2-like / Endonuclease/exonuclease/phosphatase superfamily / 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
Probable exodeoxyribonuclease III protein XthA / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Mycobacterium tuberculosis (bacteria)
Contact author
  • Ravishankar Ramachandran (CSIR-Central Drug Research Institute)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #2353
Type: dummy / Software: (dammif) / Radius of dummy atoms: 8.60 A / Symmetry: P1 / Chi-square value: 1.498
Model #2354
Type: dummy / Software: (DAMFILT) / Radius of dummy atoms: 6.75 A / Symmetry: P1 / Chi-square value: 1.498

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Sample

SampleName: DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA)
Specimen concentration: 2.5 mg/ml / Entity id: 1276 / 1277
BufferName: 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol (BME)
pH: 8
Entity #1276Name: MtbLigA / Type: 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 #1277Name: MtbXthA / Type: protein / Description: Probable exodeoxyribonuclease III protein XthA / Formula weight: 32.931 / Num. of mol.: 1 / Source: Mycobacterium tuberculosis / References: UniProt: A0A0T9L251
Sequence: MPDGTIDGGH PQRPASPRLR SPLLRLATWN VNSIRTRLDR VLDWLGRADV DVLAMQETKC PDGQFPALPL FELGYDVAHV GFDQWNGVAI ASRVGLDDVR VGFDGQPSWS GKPEVAATTE ARALGATCGG IRVWSLYVPN GRALDDPHYT YKLDWLAALR DTAEGWLRDD ...Sequence:
MPDGTIDGGH PQRPASPRLR SPLLRLATWN VNSIRTRLDR VLDWLGRADV DVLAMQETKC PDGQFPALPL FELGYDVAHV GFDQWNGVAI ASRVGLDDVR VGFDGQPSWS GKPEVAATTE ARALGATCGG IRVWSLYVPN GRALDDPHYT YKLDWLAALR DTAEGWLRDD PAAPIALMGD WNIAPTDDDV WSTEFFAGCT HVSEPERKAF NAIVDAQFTD VVRPFTPGPG VYTYWDYTQL RFPKKQGMRI DFILGSPALA ARVMDAQIVR EERKGKAPSD HAPVLVDLHA GHHHHHH

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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: DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein MtbXthA
Measurement date: May 13, 2017 / Storage temperature: 4 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /
MinMax
Q0.0308 4.94
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 537 /
MinMax
Q0.14 2.68
P(R) point1 537
R0 23.86
Result
Type of curve: single_conc /
ExperimentalPorod
MW112 kDa-
Volume-662 nm3

P(R)GuinierGuinier error
Forward scattering, I0201.6 197.66 0.46
Radius of gyration, Rg6.663 nm6.24 nm0.02

MinMax
D-23.86
Guinier point24 38

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