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

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Basic information

Entry
Database: PDB / ID: 8hhh
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: 3.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)58,5123
Polymers58,5123
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-41 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.290, 54.320, 179.261
Angle α, β, γ (deg.)90.000, 94.510, 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, A9X72_20810, ACU57_16060, BGM66_003029, BN17_45151, BO068_001919, BON68_06480, BON72_08970, BON73_04910, BON74_02170, BON75_16740, BON76_15060, BON77_21520, BON80_15910, BON89_27020, ...Gene: ftsQ, A9X72_20810, ACU57_16060, BGM66_003029, BN17_45151, BO068_001919, BON68_06480, BON72_08970, BON73_04910, BON74_02170, BON75_16740, BON76_15060, BON77_21520, BON80_15910, BON89_27020, BON93_20085, BON94_26730, BvCmsHHP019_03716, C5Y87_12070, CCS08_22990, CR538_21045, CTR35_001627, DAH19_13315, DAH50_07465, DS732_05370, DTL43_06330, DXT70_08670, E2119_07785, E2134_11600, E4K51_06165, E5P23_04335, E5P31_03955, E5P32_08015, E5P35_00730, E5P36_04260, E5P39_13665, E5P40_07375, E5P41_14185, E5P42_01010, E5P43_09200, E5P44_09730, E5P45_08355, E5P46_13085, E5P47_04370, E5P48_12150, E5P49_11070, E5P50_01390, E5S36_10750, E5S51_07905, EI021_04715, EIZ93_07570, EL79_3779, EL80_3726, ELT20_04095, ELT41_01600, ELX85_12445, F2N20_00540, F2N31_00540, F9V24_01135, FJQ40_06395, FOI11_013215, FOI11_22465, FV293_03270, FWK02_17275, GJO56_09885, GKF89_02115, GNW61_10395, GP944_03500, GP965_07730, GP979_06755, GRW05_06695, HMV95_04965, HX136_20990, IH768_05560, J0541_002403, JNP96_04660, NCTC11126_03516, NCTC13216_02643, NCTC8008_03748, NCTC8500_04640, NCTC9037_04264, NCTC9045_04807, NCTC9117_05152, NCTC9706_01498, SAMEA3751407_02594, SAMEA3752557_00798
Production host: Escherichia coli (E. coli) / References: UniProt: J7Q602
#2: Protein Cell division protein FtsB


Mass: 13397.883 Da / Num. of mol.: 1 / Mutation: E56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ygbQ, 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: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M 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: Dec 22, 2020
RadiationMonochromator: liquid-nitrogen-cooling Si double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→90.33 Å / Num. obs: 14819 / % possible obs: 99.83 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07429 / Net I/σ(I): 9.25
Reflection shellResolution: 3.3→3.56 Å / Rmerge(I) obs: 0.6163 / Num. unique obs: 1476

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Processing

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

8hhg


Resolution: 3.3→34.69 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.307 681 4.6 %
Rwork0.2756 14134 -
obs0.277 14815 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 279.05 Å2 / Biso mean: 127.6639 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.3→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 0 0 3277
Num. residues----409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.3002-3.55470.3771470.37232787
3.5547-3.9120.30731480.29942800
3.912-4.47710.29121290.24662790
4.4771-5.63680.26611500.26992815
5.6368-34.690.32071070.25992942
Refinement TLS params.Method: refined / Origin x: -17.5432 Å / Origin y: -4.0766 Å / Origin z: -16.0345 Å
111213212223313233
T0.5272 Å20.1274 Å20.0127 Å2-0.7036 Å20.1008 Å2--0.655 Å2
L1.2815 °21.3206 °2-0.8217 °2-1.8528 °2-0.7586 °2--1.6518 °2
S-0.1028 Å °-0.3139 Å °-0.0222 Å °0.1328 Å °-0.125 Å °-0.0704 Å °-0.4635 Å °0.6468 Å °0.1711 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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