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- PDB-7dma: Crystal structure of FliM middle domain (46-231) with R49P substi... -
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Open data
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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 | ||||||||||||||||||
![]() | (Flagellar motor switch protein FliM) x 2 | ||||||||||||||||||
![]() | MOTOR PROTEIN / Flagellar motor protein | ||||||||||||||||||
Function / homology | ![]() bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Takekawa, N. / Homma, M. / Imada, K. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.4 KB | Display | ![]() |
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PDB format | ![]() | 41.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.7 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dm9C ![]() 5x0zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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