[English] 日本語
Yorodumi
- SASDBN4: Callose synthase (AtGSLO5-IL) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDBN4
SampleCallose synthase
  • Callose synthase (protein), AtGSLO5-IL, Arabidopsis thaliana
Function / homology
Function and homology information


defense response by callose deposition / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / (1->3)-beta-D-glucan biosynthetic process / 1,3-beta-D-glucan synthase complex / salicylic acid mediated signaling pathway / leaf morphogenesis / defense response by callose deposition in cell wall / : / leaf senescence ...defense response by callose deposition / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / (1->3)-beta-D-glucan biosynthetic process / 1,3-beta-D-glucan synthase complex / salicylic acid mediated signaling pathway / leaf morphogenesis / defense response by callose deposition in cell wall / : / leaf senescence / innate immune response-activating signaling pathway / pollen development / response to fungus / glucosyltransferase activity / plasmodesma / defense response to fungus / defense response / regulation of cell shape / membrane => GO:0016020 / defense response to bacterium / Golgi apparatus / plasma membrane
Similarity search - Function
Glycosyl transferase, family 48 / 1,3-beta-glucan synthase subunit FKS1-like, domain-1 / 1,3-beta-glucan synthase component / 1,3-beta-glucan synthase subunit FKS1, domain-1 / 1,3-beta-glucan synthase subunit FKS1
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #520
Type: other / Software: (2.7.1) / Radius of dummy atoms: 1.90 A / Symmetry: P8 / Chi-square value: 1.055
Model #521
Type: dummy / Software: (r6669) / Radius of dummy atoms: 6.30 A / Symmetry: P8 / Chi-square value: 1.278 / P-value: 0.050400

-
Sample

SampleName: Callose synthase / Specimen concentration: 1 mg/ml
BufferName: Tris, 50 mM NaCl / pH: 7.3 / Composition: 50 mM NaCl
Entity #336Name: AtGSLO5-IL / Type: protein / Description: Callose synthase / Formula weight: 79.092 / Num. of mol.: 8 / Source: Arabidopsis thaliana / References: UniProt: Q9ZT82
Sequence: MASRGSHHHH HHGAGDRGPE FELGTRGSCA VVGLFDHLGE IRDMGQLRLR FQFFASAIQF NLMPEEQLLN ARGFGNKFKD GIHRLKLRYG FGRPFKKLES NQVEANKFAL IWNEIILAFR EEDIVSDREV ELLELPKNSW DVTVIRWPCF LLCNELLLAL SQARELIDAP ...Sequence:
MASRGSHHHH HHGAGDRGPE FELGTRGSCA VVGLFDHLGE IRDMGQLRLR FQFFASAIQF NLMPEEQLLN ARGFGNKFKD GIHRLKLRYG FGRPFKKLES NQVEANKFAL IWNEIILAFR EEDIVSDREV ELLELPKNSW DVTVIRWPCF LLCNELLLAL SQARELIDAP DKWLWHKICK NEYRRCAVVE AYDSIKHLLL SIIKVDTEEH SIITVFFQII NQSIQSEQFT KTFRVDLLPK IYETLQKLVG LVNDEETDSG RVVNVLQSLY EIATRQFFIE KKTTEQLSNE GLTPRDPASK LLFQNAIRLP DASNEDFYRQ VRRLHTILTS RDSMHSVPVN LEARRRIAFF SNSLFMNMPH APQVEKMMAF SVLTPYYSEE VVYSKEQLRN ETEDGISTLY YLQTIYADEW KNFKERMHRE GIKTDSELWT TKLRDLRLWA SYRGQTLART VRGMMYYYRA LKMLAFLDSA SEMDIREGAQ ELGSVRNLQG ELGGQSDGFV SENDRSSLSR ASSSVSTLYK GHEYGTALMK FTYVVACQIY GSQKAKKEPQ AEEILYLMKQ NEALRIAYVD EVPAGRGETD YYSVLVKYDH QLEKEVEIFR VKLPGPVKLG EGKPENQNHA MIFTRGDAVQ TIDMNQDSYF EEALKMRNLL QEYNHYHGIR KPTILGVRHA HGLSAWSHPQ FEK

-
Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
DetectorName: Pilatus 2M
Scan
Title: Callose / Measurement date: Jun 2, 2015 / Storage temperature: 20 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 18 / Unit: 1/nm /
MinMax
Q0.027 4.8012
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 433 /
MinMax
Q0.0718658 1.21325
P(R) point1 433
R0 30
Result
Type of curve: single_conc /
ExperimentalPorod
MW623 kDa646 kDa
Volume-1033.34 nm3

GuinierP(R)Guinier error
Forward scattering, I025374.1 --
Radius of gyration, Rg7.99 nm7.94 nm0.34

MinMaxError
D-30 3
Guinier point12 52 -

+
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