[English] 日本語
Yorodumi
- PDB-2mrw: Solution Structure of MciZ from Bacillus subtilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mrw
TitleSolution Structure of MciZ from Bacillus subtilis
ComponentsCell division factor
KeywordsCELL CYCLE / FtsZ
Function / homologyCell division inhibitor MciZ / Mother cell inhibitor of FtsZ / sporulation resulting in formation of a cellular spore / Cell division inhibitor MciZ
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsCastellen, P. / Sforca, M.L. / Zeri, A.C.M. / Gueiros-Filho, F.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: FtsZ filament capping by MciZ, a developmental regulator of bacterial division.
Authors: Bisson-Filho, A.W. / Discola, K.F. / Castellen, P. / Blasios, V. / Martins, A. / Sforca, M.L. / Garcia, W. / Zeri, A.C. / Erickson, H.P. / Dessen, A. / Gueiros-Filho, F.J.
History
DepositionJul 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division factor


Theoretical massNumber of molelcules
Total (without water)4,7861
Polymers4,7861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1minimized average structure

-
Components

#1: Protein/peptide Cell division factor / MciZ


Mass: 4785.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (synth.) Bacillus subtilis (bacteria) / References: UniProt: L8EBJ9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-1H NOESY
1422D 1H-1H TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM MciZ, 50 mM sodium phosphate, 50 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM MciZ, 50 mM sodium phosphate, 50 mM potassium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.2 mMMciZ-11
50 mMsodium phosphate-21
50 mMpotassium chloride-31
0.2 mMMciZ-42
50 mMsodium phosphate-52
50 mMpotassium chloride-62
Sample conditionsIonic strength: 0.05 / pH: 4.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift calculation
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / 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://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