+Open data
-Basic information
Entry | Database: PDB / ID: 2d4y | ||||||
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Title | Crystal structure of a 49K fragment of HAP1 (FlgK) | ||||||
Components | Flagellar hook-associated protein 1 | ||||||
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 assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 | 2d4y.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4y.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d4y_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 2d4y_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 2d4y_validation.xml.gz | 43 KB | Display | |
Data in CIF | 2d4y_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4y ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49604.293 Da / Num. of mol.: 2 / Fragment: FK49 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1J5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 5.5 Details: 14-15% PEG 8000, 20-25% isopropanol, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→75 Å / Num. all: 56302 / Num. obs: 56302 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.2 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.6 / Num. unique all: 9113 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→74.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.848 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.255 / ESU R Free: 0.202 / 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: 42.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→74.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20 /
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