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Yorodumi- PDB-5dn4: Structure of the glycoside hydrolase domain from Salmonella typhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dn4 | ||||||
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Title | Structure of the glycoside hydrolase domain from Salmonella typhimurium FlgJ | ||||||
Components | Peptidoglycan hydrolase FlgJ | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / family 73 / FlgJ / Flagella | ||||||
Function / homology | Function and homology information amidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, acting on glycosyl bonds / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / metabolic process / cell wall organization / periplasmic space Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.8 Å | ||||||
Authors | Zaloba, P. / Bailey-Elkin, B.A. / Mark, B.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Plos One / Year: 2016 Title: Structural and Biochemical Insights into the Peptidoglycan Hydrolase Domain of FlgJ from Salmonella typhimurium. Authors: Zaloba, P. / Bailey-Elkin, B.A. / Derksen, M. / Mark, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dn4.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dn4.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/5dn4 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/5dn4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19304.652 Da / Num. of mol.: 1 / Fragment: unp residues 151-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: flgJ, fla FX, flaZ, STM1182 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 Gold HTE References: UniProt: P15931, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 35 mg/ml protein in 18-22% polyethylene glycol 3350 and 0.25-0.35 M NaI |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.5 Å / Num. obs: 17650 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→28.989 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 20.33 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→28.989 Å
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Refine LS restraints |
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LS refinement shell |
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