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- PDB-8hhg: The bacterial divisome protein complex FtsB-FtsL-FtsQ -

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Basic information

Entry
Database: PDB / ID: 8hhg
TitleThe bacterial divisome protein complex FtsB-FtsL-FtsQ
Components
  • Cell division protein FtsB
  • Cell division protein FtsL
  • Cell division protein FtsQ
KeywordsMEMBRANE PROTEIN / Bacterial cell division / divisome / FtsB / FtsL / FtsQ / FtsBLQ / FtsQLB / membrane protein complex / heterotrimer
Function / homology
Function and homology information


cell septum assembly / cell septum / FtsZ-dependent cytokinesis / cell division site / plasma membrane
Similarity search - Function
Cell division protein FtsL / Cell division protein FtsL / 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 ...Cell division protein FtsL / Cell division protein FtsL / 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 / POTRA domain / POTRA domain profile.
Similarity search - Domain/homology
Cell division protein FtsL / Cell division protein FtsQ / Cell division protein FtsB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNguyen, V.H.T. / Chen, X.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome.
Authors: Nguyen, H.T.V. / Chen, X. / Parada, C. / Luo, A.C. / Shih, O. / Jeng, U.S. / Huang, C.Y. / Shih, Y.L. / Ma, C.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Cell division protein FtsQ
B: Cell division protein FtsB
L: Cell division protein FtsL


Theoretical massNumber of molelcules
Total (without water)58,5703
Polymers58,5703
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, two bands of a potential hexamer and trimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-37 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.090, 53.850, 177.418
Angle α, β, γ (deg.)90.000, 93.930, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Cell division protein FtsQ


Mass: 31467.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ftsQ / Production host: Escherichia coli (E. coli) / References: UniProt: J7Q602
#2: Protein Cell division protein FtsB


Mass: 13455.919 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ftsB / Production host: Escherichia coli (E. coli) / References: UniProt: Q1JQN6
#3: Protein Cell division protein FtsL


Mass: 13646.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ftsL / Production host: Escherichia coli (E. coli) / References: UniProt: D6II44

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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: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH 8.0, 20-35% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 28, 2020
RadiationMonochromator: liquid-nitrogen-cooling Si double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→88.5 Å / Num. obs: 17628 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.9 / Num. measured all: 131166 / Scaling rejects: 354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
3.1-3.317.51.2322376731610.8171.6100
8.77-88.56.50.06852828070.99616.296.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HHF

8hhf


Resolution: 3.1→34.452 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2858 843 4.8 %
Rwork0.2428 16703 -
obs0.2448 17546 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.55 Å2 / Biso mean: 109.3532 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.1→34.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 0 0 3281
Num. residues----409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.29410.40831060.34512771100
3.2941-3.54820.36111240.28582788100
3.5482-3.90480.2831620.2472735100
3.9048-4.46880.2791710.21872757100
4.4688-5.62630.30791350.23022812100
5.6263-34.4520.2461450.2305284098
Refinement TLS params.Method: refined / Origin x: -17.8763 Å / Origin y: -4.0685 Å / Origin z: -15.8832 Å
111213212223313233
T0.5503 Å20.0365 Å2-0.0269 Å2-0.6224 Å20.0952 Å2--0.593 Å2
L0.7939 °20.5257 °2-0.3662 °2-1.1221 °2-0.3337 °2--1.4782 °2
S-0.1307 Å °-0.2195 Å °0.0248 Å °0.0132 Å °-0.0778 Å °-0.0463 Å °-0.2562 Å °0.3953 Å °0.1965 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allQ22 - 260
2X-RAY DIFFRACTION1allB1 - 89
3X-RAY DIFFRACTION1allL39 - 119

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