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- PDB-9ljk: Structure of the periplasmic domain of MotS from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 9ljk
TitleStructure of the periplasmic domain of MotS from Bacillus subtilis
ComponentsFlagellar motor protein MotS
KeywordsMOTOR PROTEIN / bacterial flagellum / stator protein / peptidoglycan binding
Function / homologyMotility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / plasma membrane / Flagellar motor protein MotS
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsNishiuchi, K. / Takekawa, N. / Imada, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K18114 Japan
Japan Society for the Promotion of Science (JSPS)21H02443 Japan
Japan Society for the Promotion of Science (JSPS)17KT0026 Japan
Japan Society for the Promotion of Science (JSPS)23K14158 Japan
CitationJournal: Biomolecules / Year: 2025
Title: Sodium-Dependent Conformational Change in Flagellar Stator Protein MotS from Bacillus subtilis.
Authors: Takekawa, N. / Yamaguchi, A. / Nishiuchi, K. / Uehori, M. / Kinoshita, M. / Minamino, T. / Imada, K.
History
DepositionJan 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar motor protein MotS
B: Flagellar motor protein MotS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9013
Polymers41,8052
Non-polymers961
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-12 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.990, 80.730, 55.240
Angle α, β, γ (deg.)90.000, 100.440, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Flagellar motor protein MotS


Mass: 20902.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal fragment (68-242) of MotS. N-terminus Met is from the expression plasmid. C-terminal His-6 tag.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: motS, P5633_09250 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAX3RPD0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES-NaOH pH7.5, 1.26 M ammonium sulfate, protein conc 6 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→54.33 Å / Num. obs: 28678 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1861 / CC1/2: 0.655 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→54.33 Å / SU ML: 0.2488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.217 1387 4.84 %
Rwork0.1745 27283 -
obs0.1765 28670 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.73 Å2
Refinement stepCycle: LAST / Resolution: 1.89→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 5 218 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742553
X-RAY DIFFRACTIONf_angle_d0.86463443
X-RAY DIFFRACTIONf_chiral_restr0.056394
X-RAY DIFFRACTIONf_plane_restr0.0073442
X-RAY DIFFRACTIONf_dihedral_angle_d5.8166340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.960.35751450.28952709X-RAY DIFFRACTION99.65
1.96-2.040.2731490.2122709X-RAY DIFFRACTION99.83
2.04-2.130.25051390.19762729X-RAY DIFFRACTION99.65
2.13-2.240.24331420.1852682X-RAY DIFFRACTION99.58
2.24-2.380.241340.18512696X-RAY DIFFRACTION99.33
2.38-2.570.23271360.17852743X-RAY DIFFRACTION99.9
2.57-2.820.23311210.17512728X-RAY DIFFRACTION99.89
2.82-3.230.21741350.17392761X-RAY DIFFRACTION99.9
3.23-4.070.18961280.14742754X-RAY DIFFRACTION99.97
4.07-54.330.17231580.15732772X-RAY DIFFRACTION99.9

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