[English] 日本語
Yorodumi
- PDB-5jyt: NMR structure of foldswitch-stablized KaiB from Thermosynechococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jyt
TitleNMR structure of foldswitch-stablized KaiB from Thermosynechococcus elongatus
ComponentsCircadian clock protein KaiB
KeywordsSigaling protein / Circadian clock / metamorphic protein
Function / homology
Function and homology information


negative regulation of phosphorylation / circadian rhythm
Similarity search - Function
Circadian clock protein KaiB / Circadian clock protein KaiB-like / KaiB domain / KaiB domain / KaiB / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Circadian clock oscillator protein KaiB
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTseng, R.D. / LiWang, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107521 United States
CitationJournal: Science / Year: 2017
Title: Structural basis of the day-night transition in a bacterial circadian clock.
Authors: Tseng, R. / Goularte, N.F. / Chavan, A. / Luu, J. / Cohen, S.E. / Chang, Y.G. / Heisler, J. / Li, S. / Michael, A.K. / Tripathi, S. / Golden, S.S. / LiWang, A. / Partch, C.L.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Circadian clock protein KaiB


Theoretical massNumber of molelcules
Total (without water)11,7801
Polymers11,7801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Circadian clock protein KaiB


Mass: 11779.870 Da / Num. of mol.: 1
Mutation: Y8A, Y94A, N29A, G89A, D91R, FLAG tag C-terminus insertion, C-terminal truncation after Residue D99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: kaiB, tlr0482 / Plasmid: pET28b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q79V61

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HN(COCA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HBHA(CO)NH
161isotropic13D H(CCO)NH
171isotropic13D 1H-15N NOESY
182isotropic13D 1H-13C NOESY
1102isotropic13D (H)CCH-COSY
192isotropic13D HCAN
1112isotropic13D HCA(CO)N
1123isotropic13D IPAP-HNCO(CA)
1134anisotropic13D IPAP-HNCO(CA)
1193isotropic13D IPAP-HNCO
1184anisotropic13D IPAP-HNCO
1211isotropic12D 1H-15N HSQC
1202isotropic12D 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1800 uM [U-99% 13C; U-99% 15N] KaiB mutant in foldswitched state, 95% H2O/5% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)15N13C_sample_H2O95% H2O/5% D2O
solution2800 uM [U-99% 13C; U-99% 15N] KaiB mutant in foldswitched state, 99.96% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)15N13C_sample_D2O99.96% D2O
gel solution3300 uM [U-99% 13C; U-99% 15N] KaiB mutant in foldswitched state, 90% H2O/10% D2O10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)RDC_isotropic90% H2O/10% D2O
gel solution4356 uM [U-99% 13C; U-99% 15N] KaiB mutant in foldswitched state, 90% H2O/10% D2O5.16% stretched polyacrylamide gel made with 6 mm diameter 10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)RDC_aligned90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMKaiB mutant in foldswitched state[U-99% 13C; U-99% 15N]1
800 uMKaiB mutant in foldswitched state[U-99% 13C; U-99% 15N]2
300 uMKaiB mutant in foldswitched state[U-99% 13C; U-99% 15N]3
356 uMKaiB mutant in foldswitched state[U-99% 13C; U-99% 15N]4
Sample conditionsIonic strength: 0.100 mM / Label: Condition_H2O_1 / pH: 7 / Pressure: 1 atm / Temperature: 25 C

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.39Schwieters, Kuszewski, Tjandra and Clorerefinement
XippGarrett DS, Powers R, Gronenborn AM, Clore GM. J Magn Reson. 2011 Dec;213(2):357-63. doi: 10.1016/j.jmr.2011.09.007. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams http://spin.niddk.nih.gov/dgarrett/Xipp/xipp.htmlpeak picking
MARSMars - robust automatic backbone assignment of proteins Journal of Biomolecular NMR, 2004, Volume 30, Number 1, Page 11 Young-Sang Jung, Markus Zweckstetterchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.39Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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