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Yorodumi- PDB-7dm9: Crystal structure of FliM middle domain (51-229) from Vibro algin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dm9 | ||||||||||||||||||
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Title | Crystal structure of FliM middle domain (51-229) from Vibro alginolyticus | ||||||||||||||||||
Components | Flagellar motor switch protein FliMFlagellar motor switch protein | ||||||||||||||||||
Keywords | MOTOR 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 | ||||||||||||||||||
Biological species | Vibrio alginolyticus (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||||||||||||||
Authors | Takekawa, N. / Homma, M. / Imada, K. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dm9.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dm9.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/7dm9 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/7dm9 | HTTPS FTP |
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-Related structure data
Related structure data | 7dmaC 5x0zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22273.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal GSHM is a remnant of the His-tag / Source: (gene. exp.) Vibrio alginolyticus (bacteria) Gene: Vag1382_20640, VagVIO5_20640, VagYM19_20670, VagYM4_20660 Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6F8W0A1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.53 Å3/Da / Density % sol: 19.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 40 % (w/v) PEG-600, 0.1 M CHES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→73.89 Å / Num. obs: 15496 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.079 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 6 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 824 / CC1/2: 0.959 / Rpim(I) all: 0.176 / Rrim(I) all: 0.319 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X0Z Resolution: 1.71→47.72 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7224 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→47.72 Å
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Refine LS restraints |
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LS refinement shell |
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