[English] 日本語
Yorodumi
- SASDBH9: ABC transporter periplasmic substrate-binding protein TupA measur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDBH9
SampleABC transporter periplasmic substrate-binding protein TupA measured in the presence of molybdate
  • ABC transporter periplasmic substrate-binding protein (protein), Desulfovibrio alaskensis (strain G20)
Function / homology: / PBP domain / PBP superfamily domain / ABC transporter periplasmic substrate-binding protein
Function and homology information
Biological speciesDesulfovibrio alaskensis (strain G20) (bacteria)
Contact author
  • Alejandro Panjkovich (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1122
Type: mix / Software: (2.7.2) / Radius of dummy atoms: 1.90 A
Comment: Tungstate group was added manually by homology to related structures
Chi-square value: 0.899 / P-value: 0.032800
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: ABC transporter periplasmic substrate-binding protein TupA measured in the presence of molybdate
Specimen concentration: 1.00-6.00
BufferName: 5 mM Tris-HCl / pH: 7.6
Entity #584Type: protein
Description: ABC transporter periplasmic substrate-binding protein
Formula weight: 29.66 / Num. of mol.: 1 / Source: Desulfovibrio alaskensis (strain G20) / References: UniProt: Q316W1
Sequence: MAHHHHHHVD DDDKMLEVLF QGPEAPVLMM ATTTSTDNTG LLDDLAPQFT KDTGIELRWT AVGTGKALKM GENCDVDILL VHAPAAEKAF VDAGFGTART QLMYNDFVII GPAADPAGVK GMTVAAALGK IAADNAVFVS RGDNSGTHKM EKSLWKQIEG PSPEKEAWYV ...Sequence:
MAHHHHHHVD DDDKMLEVLF QGPEAPVLMM ATTTSTDNTG LLDDLAPQFT KDTGIELRWT AVGTGKALKM GENCDVDILL VHAPAAEKAF VDAGFGTART QLMYNDFVII GPAADPAGVK GMTVAAALGK IAADNAVFVS RGDNSGTHKM EKSLWKQIEG PSPEKEAWYV QTGQGMLRTI NVAAEKGGYT MTDRGTYIKY EASMDGNPPL KILVEGDKIL FNQYSAIPVN PAHCPKVKKD LADKFVNWMA SPATQKTIGD FKLMGKALFT PNAE

-
Experimental information

BeamInstrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 2M
Scan
Title: TupA measured in the presence of molybdate / Measurement date: Dec 7, 2013 / Storage temperature: 7 °C / Cell temperature: 7 °C / Exposure time: 0.045 sec. / Number of frames: 20 / Unit: 1/A /
MinMax
Q0.003 0.4443
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 431 /
MinMax
Q0.0109107 0.350324
P(R) point1 431
R0 91.61
Result
Type of curve: merged
Comments: TupA measured in the presence of molybdate, fitted to the holo-form model.
ExperimentalStandardStandard errorPorod
MW29.7 kDa26 kDa2 28 kDa
Volume---45.8 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I0756 6 744 5
Radius of gyration, Rg2.44 nm0.02 2.29 nm0.03

MinMaxError
D-9.2 3
Guinier point11 68 -

+
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