[English] 日本語
Yorodumi
- PDB-1ev0: SOLUTION STRUCTURE OF THE MINE TOPOLOGICAL SPECIFICITY DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ev0
TitleSOLUTION STRUCTURE OF THE MINE TOPOLOGICAL SPECIFICITY DOMAIN
ComponentsMINE
KeywordsCELL CYCLE / MinE / topological specificity / cell division / MinCD / minicell
Function / homology
Function and homology information


division septum site selection / regulation of division septum assembly / ATPase activator activity / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Cell division topological specificity factor MinE / Cell Cycle; Chain A / Cell division topological specificity factor MinE / Cell division topological specificity factor MinE superfamily / Septum formation topological specificity factor MinE / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division topological specificity factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, dynamical simulated annealing
AuthorsKing, G.F. / Maciejewski, M.W. / Pan, B. / Mullen, G.P.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for the topological specificity function of MinE.
Authors: King, G.F. / Shih, Y.L. / Maciejewski, M.W. / Bains, N.P. / Pan, B. / Rowland, S.L. / Mullen, G.P. / Rothfield, L.I.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1989
Title: A Division Inhibitor and a Topological Specificity Factor Coded for by the Minicell Locus Determine Proper Placement of the Division Septum in E. coli
Authors: de Boer, P.A.J. / Crossley, R.E. / Rothfield, L.I.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Proper Placement of the Escherichia coli Division Site Requires Two Functions that are Associated with Different Domains of the MinE Protein
Authors: Zhao, C.R. / de Boer, P.A.J. / Rothfield, L.I.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: The MinE ring: An FtsZ-Independent Cell Structure Required for Selection of the Correct Division Site in E. coli
Authors: Raskin, D.M. / de Boer, P.A.J.
#4: Journal: MOL.MICROBIOL. / Year: 1999
Title: The Dimerization and Topological Specificity Functions of MinE Reside in a Structurally Autonomous C-terminal Domain
Authors: King, G.F. / Rowland, S.L. / Pan, B. / Mackay, J.P. / Mullen, G.P. / Rothfield, L.I.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MINE
B: MINE


Theoretical massNumber of molelcules
Total (without water)13,4272
Polymers13,4272
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60Lowest energy and least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein MINE / CELL DIVISION TOPOLOGICAL SPECIFICITY FACTOR


Mass: 6713.656 Da / Num. of mol.: 2 / Fragment: MINE TOPOLOGICAL SPECIFICITY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P0A734

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D HNHA and 3D HNHB
1312D HMQC-J
1413D 15N-separated TOCSY
1543D 13C-separated NOESY
1623D CBCA(CO)NH and 3D HN(CA)CB
1723D HNCO
1843D (H)CCH-TOCSY
1923D C(CO)NH TOCSY and 3D HC(CO)NH TOCSY
110313C and 15N 3D edited/filtered NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Intermonomer NOEs were determined using a heterolabeled protein sample.

-
Sample preparation

Details
Solution-IDContentsSolvent system
13.0 mM U-15N,13C MinE; 20 mM sodium phosphate; 50 mM NaCl; 15 mM DTT; 1 mM EDTA; 0.02% sodium azide; 1 mM 4-(2-aminoethyl)benzenesulfonyl fluoride; pH 5.792.5% H2O, 7.5% D2O
23.5 mM U-15N MinE; 20 mM sodium phosphate; 50 mM NaCl; 15 mM DTT; 1 mM EDTA; 0.02% sodium azide; 1 mM 4-(2-aminoethyl)benzenesulfonyl fluoride; pH 5.792.5% H2O, 7.5% D2O
32.13 mM unlabeled MinE; 2.06 mM U-15N,13C MinE; 20 mM sodium phosphate; 50 mM NaCl; 15 mM DTT; 1.5 mM EDTA; 0.02% sodium azide; 0.2 mM PMSF; pH 5.795% H2O/5% D2O
43.0 mM U-15N,13C MinE; 20 mM sodium phosphate; 50 mM NaCl; 15 mM DTT; 1.5 mM EDTA; 0.02% sodium azide; 0.2 mM PMSF; pH 5.7100% D2O
Sample conditionsIonic strength: 0.075 / pH: 5.7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular Simulationsprocessing
XEASY1.3.13Tai-he Xia and Christian Bartelsdata analysis
DYANA1.5Peter Guentertstructure solution
X-PLOR3.851Axel Brungerrefinement
RefinementMethod: torsion angle dynamics, dynamical simulated annealing
Software ordinal: 1
Details: 900 structures were calculated using torsion angle dynamics (DYANA). The best 60 structures were then refined using dynamical simulated annealing in X-PLOR.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest energy and least restraint violations
Conformers calculated total number: 60 / 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