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- PDB-7dma: Crystal structure of FliM middle domain (46-231) with R49P substi... -

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Basic information

Entry
Database: PDB / ID: 7dma
TitleCrystal structure of FliM middle domain (46-231) with R49P substitution from Vibro alginolyticus
Components(Flagellar motor switch protein FliM) x 2
KeywordsMOTOR PROTEIN / Flagellar motor protein
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term
Similarity search - Domain/homology
Flagellar motor switch protein FliM / :
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsTakekawa, N. / Homma, M. / Imada, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16J01859 Japan
Japan Society for the Promotion of Science (JSPS)JP17J11237 Japan
Japan Society for the Promotion of Science (JSPS)JP20J00329 Japan
Japan Society for the Promotion of Science (JSPS)JP18K19293 Japan
Japan Society for the Promotion of Science (JSPS)JP20H03220 Japan
CitationJournal: J.Biochem. / Year: 2021
Title: A slight bending of an alpha-helix in FliM creates a counterclockwise-locked structure of the flagellar motor in Vibrio.
Authors: Takekawa, N. / Nishikino, T. / Yamashita, T. / Hori, K. / Onoue, Y. / Ihara, K. / Kojima, S. / Homma, M. / Imada, K.
History
DepositionDec 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar motor switch protein FliM
B: Flagellar motor switch protein FliM


Theoretical massNumber of molelcules
Total (without water)22,2322
Polymers22,2322
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-61 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.460, 62.990, 75.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Flagellar motor switch protein FliM


Mass: 11921.076 Da / Num. of mol.: 1 / Fragment: UNP residues 42-140 / Mutation: R49P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: fliM / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6F8W0A1
#2: Protein Flagellar motor switch protein FliM


Mass: 10310.676 Da / Num. of mol.: 1 / Fragment: UNP residues 141-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: fliM / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6G9WZM7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe single protein was digested at the position between A138 and E141. The distance between A138 ...The single protein was digested at the position between A138 and E141. The distance between A138 and E141 is 30.61 Angstrom. Therefore the polymer has been split in to two, chain A and chain B for curation.

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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: 1.67 Å3/Da / Density % sol: 22.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30 % (w/v) PEG-400, 0.1 M HEPES-NaOH, 0.2 M NaCl

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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: Nov 29, 2019
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→75.87 Å / Num. obs: 26243 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.093 / Net I/σ(I): 10.5
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1332 / CC1/2: 0.881 / Rpim(I) all: 0.307 / Rrim(I) all: 0.574 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X0Z

5x0z


Resolution: 1.44→48.46 Å / SU ML: 0.1511 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2018 2000 7.64 %
Rwork0.1726 24175 -
obs0.1748 26175 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.34 Å2
Refinement stepCycle: LAST / Resolution: 1.44→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 0 170 1646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781663
X-RAY DIFFRACTIONf_angle_d1.08472260
X-RAY DIFFRACTIONf_chiral_restr0.0907244
X-RAY DIFFRACTIONf_plane_restr0.0064301
X-RAY DIFFRACTIONf_dihedral_angle_d22.5818645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.29441420.23181719X-RAY DIFFRACTION99.89
1.48-1.520.2241390.20291670X-RAY DIFFRACTION99.94
1.52-1.560.29091390.19621690X-RAY DIFFRACTION100
1.56-1.610.21621420.18161714X-RAY DIFFRACTION99.89
1.61-1.670.23821400.18541684X-RAY DIFFRACTION99.95
1.67-1.740.23781430.17231734X-RAY DIFFRACTION99.95
1.74-1.820.18651390.17131679X-RAY DIFFRACTION99.89
1.82-1.910.20531410.16641704X-RAY DIFFRACTION99.95
1.91-2.030.20371430.16351723X-RAY DIFFRACTION100
2.03-2.190.20131420.15661732X-RAY DIFFRACTION100
2.19-2.410.18791450.16311737X-RAY DIFFRACTION99.95
2.41-2.760.19981430.17191737X-RAY DIFFRACTION99.95
2.76-3.480.16561480.16581782X-RAY DIFFRACTION100
3.48-48.460.20871540.17871870X-RAY DIFFRACTION99.85

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