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Yorodumi- PDB-5xlj: Crystal structure of the flagellar cap protein flid D2-D3 domains... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xlj | ||||||
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Title | Crystal structure of the flagellar cap protein flid D2-D3 domains from serratia marcescens in Space group P432 | ||||||
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 / cell adhesion / extracellular region Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cho, S.Y. / Song, W.S. / Hong, H.J. / Yoon, S.I. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Tetrameric structure of the flagellar cap protein FliD from Serratia marcescens. Authors: Cho, S.Y. / Song, W.S. / Hong, H.J. / Lee, G.S. / Kang, S.G. / Ko, H.J. / Kim, P.H. / 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 | 5xlj.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xlj.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/5xlj ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xlj | HTTPS FTP |
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-Related structure data
Related structure data | 5xlkC 5h5wS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21820.078 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 71-272 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: AR325_17470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QFX8 | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: 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: 3.33 Å3/Da / Density % sol: 63.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 6% PEG 6000, 2.0M sodium chloride |
-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: Dec 18, 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: 1.9→30 Å / Num. obs: 24119 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.517 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H5W Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.936 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / 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: 22.631 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→30 Å
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Refine LS restraints |
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