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Yorodumi- PDB-1jyo: Structure of the Salmonella Virulence Effector SptP in Complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jyo | ||||||
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Title | Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion Chaperone SicP | ||||||
Components |
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Keywords | CHAPERONE / Salmonella / bacterial pathogenesis / infectious disease / virulence factor / type III secretion / unfolded / protein folding / SptP / SicP | ||||||
Function / homology | Function and homology information protein secretion by the type III secretion system / : / dephosphorylation / GTPase activator activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / host cell cytoplasm / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Stebbins, C.E. / Galan, J.E. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Maintenance of an unfolded polypeptide by a cognate chaperone in bacterial type III secretion. Authors: Stebbins, C.E. / Galan, J.E. | ||||||
History |
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Remark 999 | SEQUENCE An appropriate sequence database match was not available at the time of processing. The ...SEQUENCE An appropriate sequence database match was not available at the time of processing. The authors state that the gene that was originally reported to Genbank accession code 3283218 was short by 15 residues. There are two potential start sites for trasncription of this gene, and biochemical work convinced them that the protein requires the additional amino acids at the N-terminus to function optimally, and the other sequence is likely a truncation. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jyo.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jyo.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jyo ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jyo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14457.416 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O85300, UniProt: P0CL16*PLUS #2: Protein | Mass: 11966.853 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P74873 #3: 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: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M sodium chloride, 5-10% polyethylene glycol molecular weight 6000 (PEG6000), supplemented with 2mM DTT and 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.0051 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0051 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 75880 / Num. obs: 75880 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.045 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.243 / % possible all: 74.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 452315 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 74.3 % / Rmerge(I) obs: 0.243 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. reflection obs: 70014 / σ(F): 0 / Rfactor obs: 0.224 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 |