+Open data
-Basic information
Entry | Database: PDB / ID: 2d4x | |||||||||
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Title | Crystal structure of a 26K fragment of HAP3 (FlgL) | |||||||||
Components | Flagellar hook-associated protein 3 | |||||||||
Keywords | STRUCTURAL PROTEIN / Multi-domain protein / alpha-helical bundle / complex all-beta folds | |||||||||
Function / homology | Function and homology information bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region Similarity search - Function | |||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | |||||||||
Authors | Imada, K. / Matsunami, H. / Samatey, A.F. / Nagashima, S. / Namba, K. | |||||||||
Citation | Journal: To be Published Title: Structure of the bacterial flagellar hook-filament junction Authors: Imada, K. / Matsunami, H. / Yamane, M. / Samatey, A.F. / Nagashima, S. / Namba, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d4x.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4x.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4x ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4x | HTTPS FTP |
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-Related 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: 26307.973 Da / Num. of mol.: 1 / Fragment: FL26 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / References: UniProt: P16326 |
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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: 2.08 Å3/Da / Density % sol: 40.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4.2 Details: 10-20% PEG 8000, 0.2M magnesium chloride, 0.1M Phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 11, 2001 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→52 Å / Num. all: 17862 / Num. obs: 17862 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 9.4 / Num. unique all: 2577 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→51.99 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.763 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→51.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.955 Å / Total num. of bins used: 18 /
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