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Yorodumi- PDB-7dma: Crystal structure of FliM middle domain (46-231) with R49P substi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dma | ||||||||||||||||||
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Title | Crystal structure of FliM middle domain (46-231) with R49P substitution from Vibro alginolyticus | ||||||||||||||||||
Components | (Flagellar motor switch protein FliMFlagellar motor switch protein) x 2 | ||||||||||||||||||
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: 1.44 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 | 7dma.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dma.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/7dma ftp://data.pdbj.org/pub/pdb/validation_reports/dm/7dma | HTTPS FTP |
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-Related structure data
Related structure data | 7dm9C 5x0zS C: citing same article (ref.) S: Starting model for refinement |
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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: 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 |
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#2: Protein | 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 / |
Sequence details | The 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. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.67 Å3/Da / Density % sol: 22.5 % |
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Crystal grow | Temperature: 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 |
-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: 1.44→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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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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: 21.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→48.46 Å
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Refine LS restraints |
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LS refinement shell |
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