[English] 日本語
Yorodumi- PDB-2qtk: Crystal Structure of the outer membrane protein opdK from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qtk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the outer membrane protein opdK from Pseudomonas aeruginosa | ||||||
Components | Probable porin | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane protein / beta barrel / vanillate transport / Porin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Biswas, S. / Van den Berg, B. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Crystal Structure of the Outer Membrane Protein OpdK from Pseudomonas aeruginosa. Authors: Biswas, S. / Mohammad, M.M. / Movileanu, L. / van den Berg, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qtk.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qtk.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/2qtk ftp://data.pdbj.org/pub/pdb/validation_reports/qt/2qtk | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is monomer of OpdK |
-Components
#1: Protein | Mass: 42993.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Protein expression under the control of the arabinose promoter Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: Pseudomonas aeruginosa Plasmid: OpdK gene with ShlB signal sequence cloned into pB22 with 8 His tag Production host: Escherichia coli (E. coli) / Strain (production host): C43 E.Coli cells / References: UniProt: Q9HUR5 #2: Chemical | ChemComp-C8E / ( |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.99 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Classic screen condition #87 from Nextal, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2007 / Details: Platinum coated mirror |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 23772 / Num. obs: 23167 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 20.4 Å2 / Net I/σ(I): 18.29 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.7 / % possible all: 90.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.94 Å / Rfactor Rfree error: 0.023
|