[English] 日本語
Yorodumi- PDB-6u83: OmpA-like domain of FopA1 from Francisella tularensis subsp. tula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u83 | ||||||
---|---|---|---|---|---|---|---|
Title | OmpA-like domain of FopA1 from Francisella tularensis subsp. tularensis SCHU S4 | ||||||
Components | Outer membrane associated protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / outer membrane associated protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3566 Å | ||||||
Authors | Michalska, K. / Skarina, T. / Stogios, P.J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: OmpA-like domain of FopA1 from Francisella tularensis subsp. tularensis SCHU S4 Authors: Michalska, K. / Skarina, T. / Stogios, P.J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6u83.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6u83.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 6u83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u83 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u83 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5u1hS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18740.809 Da / Num. of mol.: 1 / Fragment: OmpA-like domain (UNP residues 223-393) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria) Strain: SCHU S4 / Schu 4 / Gene: fopA1, FTT_0583 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q5NH85 |
---|---|
#2: Chemical | ChemComp-EPE / |
#3: Chemical | ChemComp-1PE / |
#4: Chemical | ChemComp-DAL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 65.51 % |
---|---|
Crystal grow | Temperature: 295 K / Method: sitting drop / pH: 7.5 Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, cryoprotectant: paratone, SITTING DROP, TEMPERATURE 295K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 19, 2019 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 10225 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 55.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Net I/σ(I): 26.25 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.157 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 528 / CC1/2: 0.899 / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5U1H Resolution: 2.3566→43.5059 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.98 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.21 Å2 / Biso mean: 82.0066 Å2 / Biso min: 43.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3566→43.5059 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|