[English] 日本語
Yorodumi
- SASDFF6: Probable exodeoxyribonuclease III protein XthA, sliding beta clam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFF6
SampleProbable exodeoxyribonuclease III protein XthA, sliding beta clamp complex
  • Beta sliding clamp (protein), Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
  • Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) (protein), Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Function / homology
Function and homology information


: / exodeoxyribonuclease III / DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / peptidoglycan-based cell wall / endonuclease activity / DNA-directed DNA polymerase activity / response to antibiotic / DNA repair ...: / exodeoxyribonuclease III / DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / peptidoglycan-based cell wall / endonuclease activity / DNA-directed DNA polymerase activity / response to antibiotic / DNA repair / DNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Exodeoxyribonuclease III-like / 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 ...Exodeoxyribonuclease III-like / 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 / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / :
Similarity search - Domain/homology
Exodeoxyribonuclease III / Beta sliding clamp
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Contact author
  • Ravishankar Ramachandran (CSIR-Central Drug Research Institute)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3016
Type: dummy / Software: (DAMAVER) / Radius of dummy atoms: 3.00 A / Chi-square value: 0.774 / P-value: 0.340933

-
Sample

SampleName: Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex
Specimen concentration: 2.5 mg/ml / Entity id: 1652 / 1654
BufferName: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol / pH: 8
Entity #1652Type: 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 #1654Type: protein
Description: Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI)
Formula weight: 32.931 / Num. of mol.: 1
Source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
References: UniProt: P96273
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

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.0992 Å / Dist. spec. to detc.: 2.867 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex
Measurement date: May 15, 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: 431 /
MinMax
Q0.1826 2.22203
P(R) point1 431
R0 11.3
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.
ExperimentalPorod
MW125 kDa61 kDa
Volume-98 nm3

P(R)GuinierGuinier error
Forward scattering, I012.85 12.98 0.058
Radius of gyration, Rg3.482 nm3.48 nm0.02

MinMax
D-11.3
Guinier point32 72

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more