[English] 日本語
Yorodumi
- PDB-1yr1: Structure of the major extracytoplasmic domain of the trans isome... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yr1
TitleStructure of the major extracytoplasmic domain of the trans isomer of the bacterial cell division protein divib from geobacillus stearothermophilus
Componentscell-division initiation protein
KeywordsCELL CYCLE / cell-division initiation protein / DIVIB / FTSQ / DIVISOME
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / cell division site / plasma membrane
Similarity search - Function
Rossmann fold - #10960 / Cell division protein DivIB / : / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / POTRA domain / POTRA domain profile. / Rossmann fold ...Rossmann fold - #10960 / Cell division protein DivIB / : / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / POTRA domain / POTRA domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein DivIB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics (CANDID, CYANA), simulated annealing (XPLOR)
AuthorsRobson, S.A. / King, G.F.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Domain architecture and structure of the bacterial cell division protein DivIB.
Authors: Robson, S.A. / King, G.F.
#1: Journal: J.Bacteriol. / Year: 1989
Title: Cloning and expression of a Bacillus subtilis division initiation gene for which a homolog has not been identified in another organism
Authors: Harry, E.J. / Wake, R.G.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Nucleotide sequence and insertional inactivation of a Bacillus subtilis gene that affects cell division, sporulation, and temperature sensitivity.
Authors: Beall, B. / Lutkenhaus, J.
#3: Journal: Mol.Microbiol. / Year: 1997
Title: DivIB, FtsZ and cell division in Bacillus subtilis.
Authors: Rowland, S.L. / Katis, V.L. / Partridge, S.R. / Wake, R.G.
#4: Journal: J.Bacteriol. / Year: 1999
Title: Membrane-bound division proteins DivIB and DivIC of Bacillus subtilis function solely through their external domains in both vegetative and sporulation division.
Authors: Katis, V.L. / Wake, R.G.
History
DepositionFeb 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 16, 2012Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 999SEQUENCE DivIB fragment was subcloned as a translational fusion to the C-terminus of Schistosoma ...SEQUENCE DivIB fragment was subcloned as a translational fusion to the C-terminus of Schistosoma japonicum glutathione S-transferase. The gene sequence encoding this protein domain was cloned using chromosomal DNA from Geobacillus stearothermophilus. The sequence matches that of the corresponding domain of the DivIB ortholog from Geobacillus kaustophilus HTA426 (SWISS-PROT entry Q5L0X5_GEOKA).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cell-division initiation protein


Theoretical massNumber of molelcules
Total (without water)13,3651
Polymers13,3651
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)25 / 60lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein cell-division initiation protein / divIB / FtsQ


Mass: 13365.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: divIB / Plasmid: pSAR19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5L0X5*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1413D 15N-separated NOESY
151HNHA
161HNHB

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DivIB, 150 mM NaCl, 10 mM sodium phosphate, 10 micromolar EDTA, 10 micromolar 4-(2-aminoethyl)benzenesulfonyl flouride (AEBSF), 0.02% sodium azide, pH 6.0, 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
21 mM DivIB, 150 mM NaCl, 10 mM sodium phosphate, 10 micromolar EDTA, 10 micromolar 4-(2-aminoethyl)benzenesulfonyl flouride (AEBSF), 0.02% sodium azide, pH 6.0, 100% D2O100% D2O
Sample conditionsIonic strength: 0.16 / pH: 6 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Frank Delaglioprocessing
XEASY1.3.13Tai-he Xia and Christian Bartelsdata analysis
CANDID1.1Peter Guntertstructure solution
CYANA1.1Peter Guntertstructure solution
XPLOR3.1Axel T. Brungerrefinement
RefinementMethod: torsion angle dynamics (CANDID, CYANA), simulated annealing (XPLOR)
Software ordinal: 1
Details: The structures are based on a total of 2709 NOE-derived distance restraints, 82 restraints defining 41 hydrogen bonds, and 196 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 60 / Conformers submitted total number: 25

+
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