[English] 日本語
Yorodumi
- SASDB85: Self-processing module of iron-regulated protein FrpC (415-591) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDB85
SampleSelf-processing module of iron-regulated protein FrpC (415-591)
  • Iron-regulated protein FrpC (amino acids 415-591) (protein), FrpC:415-591, Neisseria meningitidis serogroup B
Function / homology
Function and homology information


cell outer membrane / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Iron-regulated protein FrpC
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Contact author
  • Vojtěch Kubáň (MUNI, Masaryk University; Research group Structure and Dynamics of Proteins., Brno, Czech Republic)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #562
Type: atomic / Software: NMR (20 structure) / Radius of dummy atoms: 1.90 A / Chi-square value: XXX / P-value: 0.000620

-
Sample

SampleName: Self-processing module of iron-regulated protein FrpC (415-591)
Specimen concentration: 1.25-5.00
BufferName: Tris / Concentration: 5.00 mM / pH: 7.4 / Composition: 50 mM NaCl, 10 mM CaCl2, 0.1% NaN3
Entity #359Name: FrpC:415-591 / Type: protein
Description: Iron-regulated protein FrpC (amino acids 415-591)
Formula weight: 18.698 / Num. of mol.: 1 / Source: Neisseria meningitidis serogroup B / References: UniProt: Q9JYV5
Sequence:
PLALDLDGDG IETVATKGFS GSLFDHNRDG IRTATGWVSA DDGLLVRDLN GNGIIDNGAE LFGDNTKLAD GSFAKHGYAA LAELDSNGDN IINAADAAFQ SLRVWQDLNQ DGISQANELR TLEELGIQSL DLAYKDVNKN LGNGNTLAQQ GSYTKTNGTT AKMGDLLLAA DNLHSRFLE

-
Experimental information

BeamInstrument name: Rigaku BioSAXS-1000 / Type of source: X-ray in house / Wavelength: 0.1542 Å
Scan
Title: Self-processing module of FrpC (415-591) / Measurement date: Oct 3, 2013 / Storage temperature: 30 °C / Cell temperature: 30 °C / Exposure time: 600 sec. / Number of frames: 4 / Unit: 1/nm /
MinMax
Q0.0804 4.9895
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 311 /
MinMax
Q0.0181161 0.465841
P(R) point1 311
R0 45.07
Result
Type of curve: single_conc /
ExperimentalPorod
MW18.4 kDa-
Volume-20.5 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.1355 0.0005 0.14 0.0007
Radius of gyration, Rg1.643 nm0.005 1.7 nm0.05

MinMax
D-4.51
Guinier point16 47

+
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