[English] 日本語
Yorodumi
- SASDGU5: The C-terminal cell-surface signaling domain of the Pseudomonas c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGU5
SampleThe C-terminal cell-surface signaling domain of the Pseudomonas capeferrum anti-sigma regulator PupR in complex with the outer membrane transporter PupB N-terminal signaling domain
  • PupR protein (protein), PupR, Pseudomonas putida
  • Ferric-pseudobactin BN7/BN8 receptor (protein), PupB, Pseudomonas putida
Function / homology
Function and homology information


: / sigma factor antagonist activity / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane => GO:0016020
Similarity search - Function
FecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / TonB-dependent receptor-like / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site ...FecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / TonB-dependent receptor-like / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
Ferric-pseudobactin BN7/BN8 receptor / PupR protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
Contact author
  • Jaime Jensen (Vanderbilt University)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3796
Type: dummy / Software: (DAMFILT 5.0 (r4547)) / Radius of dummy atoms: 2.25 A / Chi-square value: 1.282 / P-value: 0.525353
Model #3797
Type: atomic / Chi-square value: 3.60827836327718

-
Sample

SampleName: The C-terminal cell-surface signaling domain of the Pseudomonas capeferrum anti-sigma regulator PupR in complex with the outer membrane transporter PupB N-terminal signaling domain
Specimen concentration: 12.8 mg/ml / Entity id: 1893 / 1894
BufferName: 25 mM HEPES 400 mM LiCl 10% v/v glycerol / pH: 7.5
Entity #1893Name: PupR / Type: protein / Description: PupR protein / Formula weight: 24.124 / Num. of mol.: 1 / Source: Pseudomonas putida / References: UniProt: Q52209
Sequence: GAMGQDWRAD YHSRIGEQRR LTLADGTQVQ LNTDSALNVA FDQQARRLRL VRGEMLITRP ALADSRPLWV DTEHGRLEST LAQFNVRLHG QHTQATVYQG SVALQPALHA YPPILLGAGE QASFNQQGLL ARQAVAAVAP AWSQGMLVAQ GQPLAAFIED LARYRRGHLA ...Sequence:
GAMGQDWRAD YHSRIGEQRR LTLADGTQVQ LNTDSALNVA FDQQARRLRL VRGEMLITRP ALADSRPLWV DTEHGRLEST LAQFNVRLHG QHTQATVYQG SVALQPALHA YPPILLGAGE QASFNQQGLL ARQAVAAVAP AWSQGMLVAQ GQPLAAFIED LARYRRGHLA CDPALAGLRV SGTFPLENTD KIIAAVAETL QLEVQHFTRY WVTLKPRMA
Entity #1894Name: PupB / Type: protein / Description: Ferric-pseudobactin BN7/BN8 receptor / Formula weight: 8.101 / Num. of mol.: 1 / Source: Pseudomonas putida / References: UniProt: P38047
Sequence:
gsAQADFDIP AGPLAPALAH FGQSAHILLS YPTALTEGRS TSGLAGRFDI DQGLAILLAG TGLEASRGAN ASYSLQASAS TG

-
Experimental information

BeamInstrument name: Advanced Photon Source (APS), Argonne National Laboratory BioCAT 18ID
City: Lemont, IL / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.103 Å / Dist. spec. to detc.: 3.5 mm
DetectorName: Pilatus3 X 1M / Pixsize x: 0.172 mm
Scan
Title: The C-terminal cell-surface signaling domain of the Pseudomonas capeferrum anti-sigma regulator PupR in complex with the outer membrane transporter PupB N-terminal signaling domain
Measurement date: Mar 16, 2016 / Cell temperature: 25 °C / Unit: 1/A /
MinMax
Q0.0244 0.3896
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 470 /
MinMax
Q0.0233 0.3089
P(R) point23 492
R0 86.72
Result
Type of curve: sec /
ExperimentalPorod
MW40 kDa32.6 kDa
Volume-55.5 nm3

P(R)GuinierGuinier error
Forward scattering, I045.02 44.27 0.28
Radius of gyration, Rg2.59 nm2.52 nm0.022

MinMax
D-8.67
Guinier point23 88

+
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://pdbjlvh1.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