SASDDD8: class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III

Basic information

• Entry: Database: SASBDB / ID: SASDDD8

Sample

class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III

• Probable exodeoxyribonuclease III protein XthA (protein), Mycobacterium tuberculosis

Function / homology

Function:

: / exodeoxyribonuclease III / endonuclease activity / DNA repair / DNA binding

Domain/homology:

Exodeoxyribonuclease III-like / 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 / Endonuclease/exonuclease/phosphatase superfamily

Component:

Probable exodeoxyribonuclease III protein XthA

• Biological species: Mycobacterium tuberculosis (bacteria)

Contact author

• Ravishankar Ramachandran (CSIR-Central Drug Research Institute)

Models

• Model #2079: ; Type: dummy / Radius of dummy atoms: 2.00 A / Symmetry: P1 / Chi-square value: 1.361; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III; Specimen concentration: 5.3 mg/ml
• Buffer: Name: 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol / pH: 8

Entity #1089

Type: protein / Description: Probable exodeoxyribonuclease III protein XthA / Formula weight: 32.108 / 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 PAAPIALMGD WNIAPTDDDV WSTEFFAGCT HVSEPERKAF NAIVDAQFTD VVRPFTPGPG VYTYWDYTQL RFPKKQGMRI DFILGSPALA ARVMDAQIVR EERKGKAPSD HAPVLVDLHA G

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.082 Å / Dist. spec. to detc.: 1.1 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III
Measurement date: May 12, 2017 / Storage temperature: 4 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /

	Min	Max
Q	0.0308	4.9444

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 840 /

	Min	Max
Q	0.111457	4.09072
P(R) point	1	840
R	0	7.31

Result

Type of curve: single_conc
Comments: CAUTION! The SAXS data at very-low angles (s < 0.21 nm-1) have error estimates and intensities that are unrealistic for a single-concentration SAXS profile and are inconsistent with the remaining dataset.

	Experimental	Porod
MW	35.65 kDa	-
Volume	-	56.2 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	13.54	13.63	0.013
Radius of gyration, Rg	2.353 nm	2.37 nm	0.012

	Min	Max
D	-	7.31
Guinier point	22	110