[English] 日本語
Yorodumi
- SASDBS6: Apo form of full length ObgE from E.coli (ObgE_FL) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDBS6
SampleApo form of full length ObgE from E.coli (ObgE_FL)
  • GTPase ObgE/CgtA (protein), ObgE_FL, Escherichia coli (strain K12)
Function / homology
Function and homology information


guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / GDP binding / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / GDP binding / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / rRNA binding / GTPase activity / GTP binding / magnesium ion binding / DNA binding / cytosol
Similarity search - Function
GTP1/OBG, conserved site / GTP1/OBG family signature. / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. ...GTP1/OBG, conserved site / GTP1/OBG family signature. / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEscherichia coli (strain K12) (bacteria)
CitationDate: 2017 Feb 21
Title: Structural and Biochemical Analysis of Escherichia coli ObgE, a Central Regulator of Bacterial Persistence
Authors: Gkekas S / Singh R / Shkumatov A / Messens J / Fauvart M / Verstraeten N / Michiels J
Contact author
  • Alexander V. Shkumatov (VUB, Vrije Universiteit Brussel, Pleinlaan 2 1050 Brussel)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #725
Type: dummy / Software: DAMMIN (r6293) / Radius of dummy atoms: 3.50 A / Symmetry: P1 / Chi-square value: 13.099
Search similar-shape structures of this assembly by Omokage search (details)
Model #743
Type: atomic / Software: RANCH/FULCHER/GAJOE / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 11.336
Search similar-shape structures of this assembly by Omokage search (details)
Model #744
Type: atomic / Software: RANCH/FULCHER/GAJOE / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 11.336
Search similar-shape structures of this assembly by Omokage search (details)
Model #745
Type: atomic / Software: RANCH/FULCHER/GAJOE / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 11.336
Search similar-shape structures of this assembly by Omokage search (details)
Model #746
Type: atomic / Software: RANCH/FULCHER/GAJOE / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 11.336
Search similar-shape structures of this assembly by Omokage search (details)
Model #747
Type: atomic / Software: RANCH/FULCHER/GAJOE / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 11.336
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Apo form of full length ObgE from E.coli (ObgE_FL) / Specimen concentration: 10 mg/ml
BufferName: 20 mM Hepes , 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT
pH: 7.5
Entity #420Name: ObgE_FL / Type: protein / Description: GTPase ObgE/CgtA / Formula weight: 44.441 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P42641
Sequence: MKFVDEASIL VVAGDGGNGC VSFRREKYIP KGGPDGGDGG DGGDVWMEAD ENLNTLIDYR FEKSFRAERG QNGASRDCTG KRGKDVTIKV PVGTRVIDQG TGETMGDMTK HGQRLLVAKG GWHGLGNTRF KSSVNRTPRQ KTNGTPGDKR ELLLELMLLA DVGMLGMPNA ...Sequence:
MKFVDEASIL VVAGDGGNGC VSFRREKYIP KGGPDGGDGG DGGDVWMEAD ENLNTLIDYR FEKSFRAERG QNGASRDCTG KRGKDVTIKV PVGTRVIDQG TGETMGDMTK HGQRLLVAKG GWHGLGNTRF KSSVNRTPRQ KTNGTPGDKR ELLLELMLLA DVGMLGMPNA GKSTFIRAVS AAKPKVADYP FTTLVPSLGV VRMDNEKSFV VADIPGLIEG AAEGAGLGIR FLKHLERCRV LLHLIDIDPI DGTDPVENAR IIISELELYS QDLATKPRWL VFNKIDLLDK VEAEEKAKAI AEALGWEDKY YLISAASGLG VKDLCWDVMT FIIENPVAQA EEAKQPEKVE FMWDDYHRQQ LEEIAEEDDE DWDDDWDEDD EEGVEFIYKR SAWSHPQFEK

-
Experimental information

BeamInstrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.103 Å / Dist. spec. to detc.: 1.987 mm
DetectorName: AVIEX / Type: CCD
Scan
Title: Apo form of full length ObgE from E.coli (ObgE_FL) / Measurement date: Jun 17, 2015 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 2.8 sec. / Number of frames: 255 / Unit: 1/A /
MinMax
Q0.0061 0.5535
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 981 /
MinMax
Q0.0158189 0.514514
P(R) point1 981
R0 181
Result
Type of curve: other
Comments: The sample protein includes a C-terminal Strep-tag; frames corresponding to the peak in HPLC-SAXS run were averaged using DATAVER v0.2 (r3709)
ExperimentalPorod
MW55.4 kDa60 kDa
Volume-102 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.03904 0.0003 0.0383 2.7E-5
Radius of gyration, Rg3.96 nm0.1 3.7 nm0.1

MinMax
D-18.1
Guinier point18 46

+
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