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Yorodumi- PDB-5zj0: Crystal structure of Xanthomonas campestris FlgL (space group C2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zj0 | ||||||
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Title | Crystal structure of Xanthomonas campestris FlgL (space group C2) | ||||||
Components | Flagellar hook protein FlgL | ||||||
Keywords | STRUCTURAL PROTEIN / flagellum / junction | ||||||
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 | Xanthomonas campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hong, H.J. / Kim, T.H. / Song, W.S. / Yoon, S.I. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Crystal structure of FlgL and its implications for flagellar assembly Authors: Hong, H.J. / Kim, T.H. / Song, W.S. / Ko, H.J. / Lee, G.S. / Kang, S.G. / 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 | 5zj0.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zj0.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/5zj0 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/5zj0 | HTTPS FTP |
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-Related structure data
Related structure data | 5ziyC 5zizSC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34016.879 Da / Num. of mol.: 1 / Fragment: UNP residues 4-364 / Mutation: A340V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: RT95_19740 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A0D0KCW5, UniProt: A0A3E1L4S6*PLUS |
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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: 2.32 Å3/Da / Density % sol: 47.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 19% PEG6000, 0.1M Hepes, pH 7.0, and 1.0M lithium chloride |
-Data collection
Diffraction | Mean temperature: 291 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: Jul 25, 2017 |
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: 24596 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1209 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZIZ Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.096 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / 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: 31.038 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→30 Å
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Refine LS restraints |
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