+Open data
-Basic information
Entry | Database: PDB / ID: 5h72 | ||||||
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Title | Structure of the periplasmic domain of FliP | ||||||
Components | Flagellar biosynthetic protein FliP | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Flagellar protein export | ||||||
Function / homology | Function and homology information bacterial-type flagellum organization / bacterial-type flagellum basal body / protein secretion / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Fukumura, T. / Kawaguchi, T. / Saijo-Hamano, Y. / Namba, K. / Minamino, T. / Imada, K. | ||||||
Citation | Journal: PLoS Biol. / Year: 2017 Title: Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex Authors: Fukumura, T. / Makino, F. / Dietsche, T. / Kinoshita, M. / Kato, T. / Wagner, S. / Namba, K. / Imada, K. / Minamino, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus Authors: Fukumura, T. / Furukawa, Y. / Kawaguchi, T. / Saijo-Hamano, Y. / Namba, K. / Imada, K. / Minamino, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h72.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h72.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/5h72 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h72 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9433.692 Da / Num. of mol.: 8 / Fragment: periplasmic fragment, UNP residues 110-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: fliP, TM_0698, Tmari_0698 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZG2 #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: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 0.1M phosphate-citrate pH 4.4, 36% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 2, 2012 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.6 Å / Num. obs: 30262 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→42.923 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.923 Å
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Refine LS restraints |
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LS refinement shell |
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