[English] 日本語
Yorodumi
- SASDB94: Suppressor of Copper Sensitivity C protein (ScsC) from Proteus mi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDB94
SampleSuppressor of Copper Sensitivity C protein (ScsC) from Proteus mirabilis
  • Suppressor of Copper Sensitivity C protein (protein), PmScsC (DsbA-like), Proteus mirabilis ATCC 29906
Function / homology:
Function and homology information
Biological speciesProteus mirabilis ATCC 29906 (bacteria)
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 #486
Type: atomic / Radius of dummy atoms: 1.90 A / Symmetry: P3 / Chi-square value: 0.86
Search similar-shape structures of this assembly by Omokage search (details)
Model #487
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.251 / P-value: 0.020808
Search similar-shape structures of this assembly by Omokage search (details)
Model #489
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.251 / P-value: 0.020808
Search similar-shape structures of this assembly by Omokage search (details)
Model #490
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.251 / P-value: 0.020808
Search similar-shape structures of this assembly by Omokage search (details)
Model #491
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.251 / P-value: 0.020808
Search similar-shape structures of this assembly by Omokage search (details)
Model #492
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.251 / P-value: 0.020808
Search similar-shape structures of this assembly by Omokage search (details)
Model #493
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.251 / P-value: 0.020808
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Suppressor of Copper Sensitivity C protein (ScsC) from Proteus mirabilis
Specimen concentration: 2.15-8.85
BufferName: 25 mM HEPES 150mM NaCl 1mM DTT / Concentration: 25.00 mM / pH: 7.5 / Composition: 150mM NaCl, 1mM DTT
Entity #318Name: PmScsC (DsbA-like) / Type: protein / Description: Suppressor of Copper Sensitivity C protein / Formula weight: 24.567 / Num. of mol.: 3 / Source: Proteus mirabilis ATCC 29906 / References: UniProt: C2LPE2
Sequence: AALNAAQEKE VRALVRDTLV SNPEILEEAI MALQTKKADE QQAQFRQALA SEHDALYNDA ASPRIGAKDA KLVLVSFTDY NCPYCKRFDP LLEKITEQYP DVAVIIKPLP FKGESSAKAS QAVLSVWKED PKAFLALHQR LMQKKTMLDN ASIEDAMKST NTSKIKLTDD ...Sequence:
AALNAAQEKE VRALVRDTLV SNPEILEEAI MALQTKKADE QQAQFRQALA SEHDALYNDA ASPRIGAKDA KLVLVSFTDY NCPYCKRFDP LLEKITEQYP DVAVIIKPLP FKGESSAKAS QAVLSVWKED PKAFLALHQR LMQKKTMLDN ASIEDAMKST NTSKIKLTDD SLKTLQNNLE LSRKLGIQGT PATVIGDTIL PGAVDYDQLE IIVKEQLAKV KK

-
Experimental information

BeamInstrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / : Australia / Shape: Point / Type of source: X-ray synchrotron / Dist. spec. to detc.: 1.6 mm
DetectorName: Pilatus 1M
Scan
Title: Suppressor of Copper Sensitive protein C / Measurement date: Feb 29, 2012 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 2 sec. / Number of frames: 14 / Unit: 1/nm /
MinMax
Q0.0863 2.4873
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 181 /
MinMax
Q0.009955 0.2487
P(R) point2 182
R0 105
Result
Type of curve: single_conc /
ExperimentalPorod
MW69.9 kDa-
Volume-92 nm3

P(R)P(R) errorGuinier
Forward scattering, I00.1006 0.00016 0.101
Radius of gyration, Rg3.6 nm0.01 3.65 nm

MinMax
D-10.5
Guinier point3 21

+
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