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- PDB-6h9o: Complex of the periplasmic domains of bacterial cell division pro... -

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Basic information

Entry
Database: PDB / ID: 6h9o
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


FtsQBL complex / divisome complex / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli S88 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3064
Polymers58,3064
Non-polymers00
Water00
1
A: Cell division protein FtsQ
B: Cell division protein FtsB


Theoretical massNumber of molelcules
Total (without water)29,1532
Polymers29,1532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cell division protein FtsQ
D: Cell division protein FtsB


Theoretical massNumber of molelcules
Total (without water)29,1532
Polymers29,1532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.221, 48.011, 131.619
Angle α, β, γ (deg.)90.00, 112.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsQ


Mass: 26269.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ftsQ, b0093, JW0091 / Production host: Escherichia coli (E. coli) / References: UniProt: P06136
#2: Protein/peptide Cell division protein FtsB


Mass: 2883.177 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Met 77 in FtsB was replaced with Norleucin (Nle) as this is a synthetic peptide
Source: (synth.) Escherichia coli S88 (bacteria) / References: UniProt: B7MKM2
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.057 M potassium thiocyanate, 10 % PEG 550 MME, 0.1 M sodium cacodylate pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15922 / % possible obs: 98.5 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.051 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2374 / CC1/2: 0.686 / Rpim(I) all: 0.488 / % possible all: 99.7

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Processing

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

2vh1


Resolution: 2.8→29.834 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 30.72
RfactorNum. reflection% reflection
Rfree0.277 1493 4.95 %
Rwork0.2299 --
obs0.2322 15922 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 0 0 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123640
X-RAY DIFFRACTIONf_angle_d1.6374919
X-RAY DIFFRACTIONf_dihedral_angle_d23.5042235
X-RAY DIFFRACTIONf_chiral_restr0.082534
X-RAY DIFFRACTIONf_plane_restr0.008643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.89040.38671710.35592697X-RAY DIFFRACTION96
2.8904-2.99360.39991430.31492727X-RAY DIFFRACTION96
2.9936-3.11330.31151570.30942661X-RAY DIFFRACTION97
3.1133-3.25480.35621430.2822667X-RAY DIFFRACTION95
3.2548-3.42620.35951010.27712718X-RAY DIFFRACTION94
3.4262-3.64050.31741320.24912497X-RAY DIFFRACTION90
3.6405-3.9210.27441330.23922569X-RAY DIFFRACTION90
3.921-4.31460.26231480.22362423X-RAY DIFFRACTION87
4.3146-4.93650.23191130.1892483X-RAY DIFFRACTION87
4.9365-6.21020.29961090.21832576X-RAY DIFFRACTION91
6.2102-29.8360.20581430.18162643X-RAY DIFFRACTION94

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