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Yorodumi- PDB-5h5w: Crystal structure of the flagellar cap protein FliD D2-D3 domains... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h5w | ||||||
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Title | Crystal structure of the flagellar cap protein FliD D2-D3 domains from Escherichia coli | ||||||
Components | Flagellar hook-associated protein 2 | ||||||
Keywords | STRUCTURAL PROTEIN / Bacterial flagellar cap protein | ||||||
Function / homology | Function and homology information bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Song, W.S. / Cho, S.Y. / Hong, H.J. / Yoon, S.I. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Self-Oligomerizing Structure of the Flagellar Cap Protein FliD and Its Implication in Filament Assembly. Authors: Song, W.S. / Cho, S.Y. / Hong, H.J. / Park, S.C. / Yoon, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h5w.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h5w.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 5h5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/5h5w ftp://data.pdbj.org/pub/pdb/validation_reports/h5/5h5w | HTTPS FTP |
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-Related structure data
Related structure data | 5h5tC 5h5vSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 5
NCS ensembles :
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-Components
#1: Protein | Mass: 20703.316 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 71-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fliD, OO96_01215 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A178ST54, UniProt: P24216*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.4 M ammonium sulfate, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 26548 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 2.15→2.19 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H5V Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→30 Å
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Refine LS restraints |
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