[English] 日本語
Yorodumi
- SASDGS5: MvaT (low salt data set) (MvaT(mutant)) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGS5
SampleMvaT (low salt data set)
  • MvaT(mutant) (protein), Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Function / homologyMvaT, DNA-binding domain / Bacterial xenogeneic silencer MvaT, C-terminal domain / negative regulation of single-species biofilm formation on inanimate substrate / negative regulation of secondary metabolite biosynthetic process / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / MvaT
Function and homology information
Biological speciesPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Contact author
  • Yann Sterckx (University of Antwerp)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3790
Type: atomic / P-value: 0.000006
Model #3791
Type: atomic / Comment: ensemble model / P-value: 0.000006

-
Sample

SampleName: MvaT (low salt data set) / Specimen concentration: 11 mg/ml
BufferName: 20 mM Bis-Tris 50 mM KCl / pH: 6
Entity #1888Type: protein / Description: MvaT(mutant) / Formula weight: 14.107 / Num. of mol.: 2
Source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
References: UniProt: Q9HW86
Sequence:
MSLINEYRAT EEAIKELQER LKSLEQDDKL CKELEDEEKL RTLDGTYQKS LRDVISLLDP DAKIGKSTRT AKAPAGKRAR KVKQYKNPHT GEVIETKGGN HKTLKEWKAK WGPEAVESWA TLLG

-
Experimental information

BeamInstrument name: ESRF BioSAXS beamline BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.81 mm
DetectorName: d / Type: PILATUS 1 M, DECTRIS / Pixsize x: 0.99 mm
Scan
Title: MvaT (low salt data set) / Measurement date: May 11, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Unit: 1/A /
MinMax
Q0.0124 0.4003
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 450 /
MinMax
Q0.0133295 0.224171
P(R) point1 450
R0 147
Result
Type of curve: sec
Comments: The protein employed in the SAS experiment contains three point mutations: K31C, F36D, and M44D. K31C was introduced to introduce a paramagnetic label, while F36D and M44D were introduced ...Comments: The protein employed in the SAS experiment contains three point mutations: K31C, F36D, and M44D. K31C was introduced to introduce a paramagnetic label, while F36D and M44D were introduced to abolish higher-order oligomerisation of the protein.
ExperimentalPorod
MW28.09 kDa27.78 kDa
Volume-47.24 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I070.31 0.1 70.04 0.1
Radius of gyration, Rg3.72 nm0.01 3.59 nm0.09

MinMax
D-14.7
Guinier point1 39

+
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