[English] 日本語
Yorodumi- PDB-3x2r: Structure of the nonameric bacterial amyloid secretion channel CsgG -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x2r | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the nonameric bacterial amyloid secretion channel CsgG | ||||||
Components | CsgG | ||||||
Keywords | MEMBRANE PROTEIN / beta-barrel / outer membrane protein / curli secretion / biofim | ||||||
Function / homology | Curli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / Prokaryotic membrane lipoprotein lipid attachment site profile. / outer membrane-bounded periplasmic space / Curli production assembly/transport component CsgG / CsgG Function and homology information | ||||||
Biological species | Escherichia coli Xuzhou21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Huang, Y. / Cao, B. / Zhao, Y. / Kou, Y. / Ni, D. / Zhang, X.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structure of the nonameric bacterial amyloid secretion channel Authors: Cao, B. / Zhao, Y. / Kou, Y. / Ni, D. / Zhang, X.C. / Huang, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3x2r.cif.gz | 661.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3x2r.ent.gz | 548.7 KB | Display | PDB format |
PDBx/mmJSON format | 3x2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x2r ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x2r | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30584.035 Da / Num. of mol.: 9 / Fragment: Chymotrypsin digest fragment / Mutation: none Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli Xuzhou21 (bacteria) / Strain: CFT073 / Gene: CDCO157_1350, csgG / Plasmid: pQLinkN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: I1ZTN7, UniProt: A0A0F6C2F5*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.93 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50mM Tris-HCl(pH8.5), 300mM MgCl2, 14% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2014 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 61340 / Num. obs: 61340 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 86.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.9→48.071 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 34.98 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.071 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 206.9173 Å / Origin y: 36.5217 Å / Origin z: 5.7516 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |