[English] 日本語
Yorodumi
- PDB-6h9n: Complex of the periplasmic domains of bacterial cell division pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h9n
TitleComplex of the periplasmic domains of bacterial cell division proteins FtsQ and FtsB
Components
  • Cell division protein FtsB
  • Cell division protein FtsQ
KeywordsCELL CYCLE / bacterial cell division / divisome
Function / homology
Function and homology information


FtsBL complex / FtsQBL complex / divisome complex / cell septum / division septum assembly / FtsZ-dependent cytokinesis / cell division site / cell division / identical protein binding / plasma membrane
Similarity search - Function
Cell division protein FtsQ/DivIB / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type ...Cell division protein FtsQ/DivIB / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / membrane protein fhac / POTRA domain / POTRA domain profile. / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsB / Cell division protein FtsQ / Cell division protein FtsB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli 55989 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKureisaite-Ciziene, D. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)U105184326 United Kingdom
CitationJournal: MBio / Year: 2018
Title: Structural Analysis of the Interaction between the Bacterial Cell Division Proteins FtsQ and FtsB.
Authors: Kureisaite-Ciziene, D. / Varadajan, A. / McLaughlin, S.H. / Glas, M. / Monton Silva, A. / Luirink, R. / Mueller, C. / den Blaauwen, T. / Grossmann, T.N. / Luirink, J. / Lowe, J.
History
DepositionAug 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein FtsQ
B: Cell division protein FtsB


Theoretical massNumber of molelcules
Total (without water)37,7032
Polymers37,7032
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-2 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.785, 93.785, 106.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Cell division protein FtsQ


Mass: 26269.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ftsQ, b0093, JW0091 / Production host: Escherichia coli (E. coli) / References: UniProt: P06136
#2: Protein Cell division protein FtsB


Mass: 11433.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 55989 (bacteria) / Gene: ftsB, EC55989_3020 / Production host: Escherichia coli (E. coli) / References: UniProt: B7LEG6, UniProt: P0A6S5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M potassium thiocyanate, 20 % PEG 550 MME, 0.1 M sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 15037 / % possible obs: 99.5 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Net I/σ(I): 22.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.702 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2155 / CC1/2: 0.821 / Rpim(I) all: 0.477 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VH1

2vh1


Resolution: 2.6→29.994 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.93
RfactorNum. reflection% reflection
Rfree0.2519 1340 4.84 %
Rwork0.2228 --
obs0.2243 15024 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 0 7 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091878
X-RAY DIFFRACTIONf_angle_d1.1622540
X-RAY DIFFRACTIONf_dihedral_angle_d22.21151
X-RAY DIFFRACTIONf_chiral_restr0.058275
X-RAY DIFFRACTIONf_plane_restr0.007333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.38911360.3762627X-RAY DIFFRACTION99
2.6929-2.80060.33391180.3422655X-RAY DIFFRACTION99
2.8006-2.9280.34331430.30372621X-RAY DIFFRACTION100
2.928-3.08220.33221340.28952618X-RAY DIFFRACTION98
3.0822-3.27510.31421110.27662666X-RAY DIFFRACTION99
3.2751-3.52760.35771450.24832611X-RAY DIFFRACTION100
3.5276-3.8820.27051370.24242661X-RAY DIFFRACTION100
3.882-4.44210.29161360.19712633X-RAY DIFFRACTION99
4.4421-5.59070.2091210.18792657X-RAY DIFFRACTION100
5.5907-29.99550.16011590.18322595X-RAY DIFFRACTION99

+
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