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- PDB-5y3z: Structure of the periplasmic domain of the MotB L119P mutant from... -

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Basic information

Entry
Database: PDB / ID: 5y3z
TitleStructure of the periplasmic domain of the MotB L119P mutant from Salmonella (crystal form 1)
ComponentsMotility protein B
KeywordsMOTOR PROTEIN / 2-LAYER SANDWICH / BACTERIAL FLAGELLUM / CELL PROJECTION / CHEMOTAXIS / FLAGELLAR ROTATION / INNER MEMBRANE / MEMBRANE PROTEIN
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile.
Similarity search - Domain/homology
ARGININE / IMIDAZOLE / Motility protein B
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTakao, M. / Kojima, S. / Sakuma, M. / Homma, M. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Structure / Year: 2018
Title: The Helix Rearrangement in the Periplasmic Domain of the Flagellar Stator B Subunit Activates Peptidoglycan Binding and Ion Influx.
Authors: Kojima, S. / Takao, M. / Almira, G. / Kawahara, I. / Sakuma, M. / Homma, M. / Kojima, C. / Imada, K.
History
DepositionJul 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Motility protein B
B: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,45610
Polymers41,4372
Non-polymers1,0188
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-27 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.130, 84.800, 86.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Motility protein B / Chemotaxis protein MotB


Mass: 20718.629 Da / Num. of mol.: 2 / Fragment: UNP residues 99-276 / Mutation: L119P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: motB, STM1922 / Variant: SJW1103 / Plasmid: PET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55892
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% PEG 3350, 0.1M imidazole-HCl, 0.15M Arg-HCl, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2010
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.4 Å / Num. obs: 22684 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1629 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZVY

2zvy


Resolution: 2→35.687 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1996 8.82 %
Rwork0.1899 --
obs0.1927 22642 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 70 151 2426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022333
X-RAY DIFFRACTIONf_angle_d0.7143147
X-RAY DIFFRACTIONf_dihedral_angle_d13.574904
X-RAY DIFFRACTIONf_chiral_restr0.026345
X-RAY DIFFRACTIONf_plane_restr0.003421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28081390.25251432X-RAY DIFFRACTION100
2.05-2.10550.26631370.23261464X-RAY DIFFRACTION100
2.1055-2.16740.21281430.21631456X-RAY DIFFRACTION100
2.1674-2.23740.24761350.20981451X-RAY DIFFRACTION100
2.2374-2.31730.22621390.20451451X-RAY DIFFRACTION100
2.3173-2.41010.23591440.19381455X-RAY DIFFRACTION100
2.4101-2.51970.25031400.19591458X-RAY DIFFRACTION100
2.5197-2.65250.24781450.20031478X-RAY DIFFRACTION100
2.6525-2.81870.23421390.20411472X-RAY DIFFRACTION100
2.8187-3.03620.22361430.19161471X-RAY DIFFRACTION100
3.0362-3.34150.20721500.18661486X-RAY DIFFRACTION100
3.3415-3.82460.17691450.17051494X-RAY DIFFRACTION100
3.8246-4.81670.19911420.15381521X-RAY DIFFRACTION100
4.8167-35.6930.23311550.19181557X-RAY DIFFRACTION98

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