[English] 日本語
Yorodumi
- SASDCJ7: C-terminal domain of DsbD from N. meningitidis (thiol-disulfide e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDCJ7
SampleC-terminal domain of DsbD from N. meningitidis
  • thiol-disulfide exchange proteinDisulfide (protein), alpha-DsbN, Wolbachia endosymbiont of Drosophila melanogaster
Function / homologyThioredoxin / Thioredoxin-like fold / Thioredoxin-like superfamily / DsbA-like disulfide oxidoreductase
Function and homology information
Biological speciesWolbachia endosymbiont of Drosophila melanogaster (bacteria)
CitationDate: 2018 Jan 1
Title: Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis
Authors: Smith R / Whitten A / Paxman J / Kahler C / Scanlon M
Contact author
  • Andrew Whitten (ANSTO, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1529
Type: dummy / Software: (5.3) / Radius of dummy atoms: 1.25 A / Chi-square value: 1.593 / P-value: 0.034800
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: C-terminal domain of DsbD from N. meningitidis / Specimen concentration: 0.30-4.50
BufferName: 25mM HEPES 150mM NaCl / pH: 6.7
Entity #793Name: alpha-DsbN / Type: protein / Description: thiol-disulfide exchange proteinDisulfide / Formula weight: 21.091 / Num. of mol.: 1 / Source: Wolbachia endosymbiont of Drosophila melanogaster / References: UniProt: Q73FL6
Sequence:
SNAARDNVTK SKISQYKDQI FDLTYPYSGN ENSSVIAVGF LDYSCGHCKA IKNDIKQLIN DGKIKYIFRD APILGNASLK AAKSALAVYF LNKEKYFDFH HAALSHKGEF SDESILDIVK NIGIDEDDFN DSIKDNADKI EQMINNSRLL VRDLGVGGTP FLIIGDSLFV GATDLNVLRK KVDELSHKQG

-
Experimental information

BeamInstrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1127 Å / Dist. spec. to detc.: 1.48 mm
DetectorName: Pilatus 1M
Scan
Title: C-terminal domain of DsbD from N. meningitidis / Measurement date: May 4, 2013 / Storage temperature: 4 °C / Cell temperature: 12 °C / Exposure time: 2 sec. / Number of frames: 30 / Unit: 1/A /
MinMax
Q0.0136 0.399
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 301 /
MinMax
Q0.01101 0.399
P(R) point2 302
R0 45
Result
Type of curve: single_conc
ExperimentalStandardStandard errorPorod
MW11.8 kDa11.8 kDa1 12 kDa
Volume---14.6 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.009905 1.1E-5 0.00997 2.0E-5
Radius of gyration, Rg14.8 nm0.1 1.53 nm0.01

MinMaxError
D-4.5 0.3
Guinier point2 44 -

+
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