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- SASDFG6: Probable exodeoxyribonuclease III protein XthA, sliding beta clam... -

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Basic information

Entry
Database: SASBDB / ID: SASDFG6
SampleProbable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex
  • Beta sliding clamp (protein), Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
  • Probable exodeoxyribonuclease III protein XthA (protein), Mycobacterium tuberculosis
  • DNA ligase A (protein), Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Function / homology
Function and homology information


: / DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / exodeoxyribonuclease III / DNA ligation / DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / peptidoglycan-based cell wall ...: / DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / exodeoxyribonuclease III / DNA ligation / DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / peptidoglycan-based cell wall / endonuclease activity / DNA replication / DNA-directed DNA polymerase activity / response to antibiotic / DNA repair / magnesium ion binding / DNA binding / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Exodeoxyribonuclease III-like / 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 ...Exodeoxyribonuclease III-like / 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. / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / RuvA domain 2-like / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / 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 / Beta sliding clamp / 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 #3033
Type: dummy / Software: (DAMAVER) / Radius of dummy atoms: 5.75 A / Chi-square value: 1.119

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Sample

SampleName: Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex
Specimen concentration: 2 mg/ml / Entity id: 1664 / 1665 / 1666
BufferName: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol / pH: 8
Entity #1664Type: protein / Description: Beta sliding clamp / Formula weight: 42.935 / Num. of mol.: 2
Source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
References: UniProt: P9WNU1
Sequence: MDAATTRVGL TDLTFRLLRE SFADAVSWVA KNLPARPAVP VLSGVLLTGS DNGLTISGFD YEVSAEAQVG AEIVSPGSVL VSGRLLSDIT RALPNKPVDV HVEGNRVALT CGNARFSLPT MPVEDYPTLP TLPEETGLLP AELFAEAISQ VAIAAGRDDT LPMLTGIRVE ...Sequence:
MDAATTRVGL TDLTFRLLRE SFADAVSWVA KNLPARPAVP VLSGVLLTGS DNGLTISGFD YEVSAEAQVG AEIVSPGSVL VSGRLLSDIT RALPNKPVDV HVEGNRVALT CGNARFSLPT MPVEDYPTLP TLPEETGLLP AELFAEAISQ VAIAAGRDDT LPMLTGIRVE ILGETVVLAA TDRFRLAVRE LKWSASSPDI EAAVLVPAKT LAEAAKAGIG GSDVRLSLGT GPGVGKDGLL GISGNGKRST TRLLDAEFPK FRQLLPTEHT AVATMDVAEL IEAIKLVALV ADRGAQVRME FADGSVRLSA GADDVGRAEE DLVVDYAGEP LTIAFNPTYL TDGLSSLRSE RVSFGFTTAG KPALLRPVSG DDRPVAGLNG NGPFPAVSTD YVYLLMPVRL PGHHHHHH
Entity #1665Type: protein / Description: Probable exodeoxyribonuclease III protein XthA / Formula weight: 30.699 / Num. of mol.: 1 / Source: Mycobacterium tuberculosis / References: UniProt: A0A0T9L251
Sequence: MRLATWNVNS VKARLPRLLA WLDETKPDVV CLQETKSAAD GFPSGDVAEL GYTTAAYGEG RWNGVAILSR VGIEDVSKSF PGEPVYQGEA PAGPGVQTQL TEPVLLAPQA RAIGATCGGI RVWSLYAPNG RTPESAHYLY KLEWFAALRD ALAAELSAGT PLVATGDYNV ...Sequence:
MRLATWNVNS VKARLPRLLA WLDETKPDVV CLQETKSAAD GFPSGDVAEL GYTTAAYGEG RWNGVAILSR VGIEDVSKSF PGEPVYQGEA PAGPGVQTQL TEPVLLAPQA RAIGATCGGI RVWSLYAPNG RTPESAHYLY KLEWFAALRD ALAAELSAGT PLVATGDYNV APTDDDVWDP SVFVGSTHVT PAERQALAEL RDLGLHDIVP TPMKGPHPYT YWDYRAGSFH KDLGMRIDLV YGNGAFAERV RSAYVDREAR KGRGPSDHAP VVVDLDHHHH HH
Entity #1666Type: protein / Description: DNA ligase A / Formula weight: 76.111 / Num. of mol.: 1
Source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
References: UniProt: P9WNV1
Sequence: MSSPDADQTA PEVLRQWQAL AEEVREHQFR YYVRDAPIIS DAEFDELLRR LEALEEQHPE LRTPDSPTQL VGGAGFATDF EPVDHLERML SLDNAFTADE LAAWAGRIHA EVGDAAHYLC ELKIDGVALS LVYREGRLTR ASTRGDGRTG EDVTLNARTI ADVPERLTPG ...Sequence:
MSSPDADQTA 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

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.0992 Å / Dist. spec. to detc.: 2.9 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex
Measurement date: May 17, 2017 / Storage temperature: 4 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /
MinMax
Q0.0308 4.9444
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 188 /
MinMax
Q0.163629 1.05055
P(R) point1 188
R0 25.33
Result
Type of curve: single_conc
Comments: The presented model shows the spatial alignment of several individually calculated models and does not fit the SAXS data. A corresponding individual model fit (individual model not provided ...Comments: The presented model shows the spatial alignment of several individually calculated models and does not fit the SAXS data. A corresponding individual model fit (individual model not provided for this entry) is shown. The sample shows signs of severe aggregation.
ExperimentalPorod
MW205 kDa313 kDa
Volume-501 nm3

P(R)GuinierGuinier error
Forward scattering, I062.81 60.38 0.23
Radius of gyration, Rg6.391 nm5.76 nm0.069

MinMax
D-25.33
Guinier point24 41

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