[English] 日本語
Yorodumi- PDB-1yj7: Crystal structure of enteropathogenic E.coli (EPEC) type III secr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yj7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of enteropathogenic E.coli (EPEC) type III secretion system protein EscJ | ||||||
Components | escJ | ||||||
Keywords | PROTEIN TRANSPORT / mixed alpha/beta / extended linker | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Yip, C.K. / Kimbrough, T.G. / Felise, H.B. / Vuckovic, M. / Thomas, N.A. / Pfuetzner, R.A. / Frey, E.A. / Finlay, B.B. / Miller, S.I. / Strynadka, N.C.J. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural characterization of the molecular platform for type III secretion system assembly. Authors: Yip, C.K. / Kimbrough, T.G. / Felise, H.B. / Vuckovic, M. / Thomas, N.A. / Pfuetzner, R.A. / Frey, E.A. / Finlay, B.B. / Miller, S.I. / Strynadka, N.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yj7.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yj7.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yj7 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yj7 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is the tetramer in the asymmetric unit. |
-Components
#1: Protein | Mass: 18518.021 Da / Num. of mol.: 4 Fragment: signal peptide-removed and non-lipidated, residues 21-190 Mutation: E62A, K63A, E64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EscJ / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8VQD3 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.41 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.2 Details: di-ammonium hydrogen phosphate, pH 8.2, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2004 / Details: mirrors | |||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 1.8→41.17 Å / Num. obs: 96428 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.082 | |||||||||
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.8→41.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||
Displacement parameters | Biso mean: 19.8 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.2 Å
| |||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å
|