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- PDB-5y40: Structure of the periplasmic domain of the MotB L119P mutant from... -

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Basic information

Entry
Database: PDB / ID: 5y40
TitleStructure of the periplasmic domain of the MotB L119P mutant from Salmonella (crystal form 2)
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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakao, M. / Kojima, S. / Sakuma, M. / Homma, M. / Imada, K.
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
C: Motility protein B
D: Motility protein B


Theoretical massNumber of molelcules
Total (without water)82,8754
Polymers82,8754
Non-polymers00
Water00
1
A: Motility protein B
B: Motility protein B


Theoretical massNumber of molelcules
Total (without water)41,4372
Polymers41,4372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-10 kcal/mol
Surface area13270 Å2
MethodPISA
2
C: Motility protein B
D: Motility protein B


Theoretical massNumber of molelcules
Total (without water)41,4372
Polymers41,4372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-15 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.950, 150.950, 91.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Motility protein B / Chemotaxis protein MotB


Mass: 20718.629 Da / Num. of mol.: 4 / 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

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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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 13% PEG 3350, 0.1M imidazole-HCl, 0.1M 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 16, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→91.4 Å / Num. obs: 26584 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3799 / % possible all: 100

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Processing

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

2zvy


Resolution: 2.8→44.077 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.19
RfactorNum. reflection% reflection
Rfree0.2501 1999 7.53 %
Rwork0.2157 --
obs0.2183 26536 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 0 0 4699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034785
X-RAY DIFFRACTIONf_angle_d0.7516465
X-RAY DIFFRACTIONf_dihedral_angle_d14.7721836
X-RAY DIFFRACTIONf_chiral_restr0.026708
X-RAY DIFFRACTIONf_plane_restr0.005866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.87010.36551390.31281719X-RAY DIFFRACTION100
2.8701-2.94770.32961410.29191720X-RAY DIFFRACTION100
2.9477-3.03450.32131390.27021714X-RAY DIFFRACTION100
3.0345-3.13240.29861410.25061729X-RAY DIFFRACTION100
3.1324-3.24430.29511400.24651720X-RAY DIFFRACTION100
3.2443-3.37410.28721410.24721727X-RAY DIFFRACTION100
3.3741-3.52760.29241430.2381749X-RAY DIFFRACTION100
3.5276-3.71350.25721400.21681726X-RAY DIFFRACTION100
3.7135-3.94610.23681430.22541752X-RAY DIFFRACTION100
3.9461-4.25050.2231420.20251738X-RAY DIFFRACTION100
4.2505-4.67780.21871440.19221766X-RAY DIFFRACTION100
4.6778-5.35370.25071450.20041791X-RAY DIFFRACTION100
5.3537-6.74120.2321470.22681796X-RAY DIFFRACTION100
6.7412-44.0820.21361540.17071890X-RAY DIFFRACTION99

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