[English] 日本語
Yorodumi- PDB-2odj: Crystal structure of the outer membrane protein OprD from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2odj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the outer membrane protein OprD from Pseudomonas aeruginosa | ||||||
Components | Porin D | ||||||
Keywords | MEMBRANE PROTEIN / outer membrane protein / beta-barrel / amino acid transport | ||||||
Function / homology | Function and homology information oligosaccharide transport / basic amino acid transport / outer membrane / porin activity / pore complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / monoatomic ion transport / serine-type peptidase activity / cell outer membrane / proteolysis Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Biswas, S. / van den Berg, B. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Structural insight into OprD substrate specificity. Authors: Biswas, S. / Mohammad, M.M. / Patel, D.R. / Movileanu, L. / van den Berg, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2odj.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2odj.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 2odj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/2odj ftp://data.pdbj.org/pub/pdb/validation_reports/od/2odj | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47443.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: oprD Plasmid details: Oprd gene with Serratia marcescens ShlB signal sequence cloned into pB22 with C-terminal His8 tag. Protein expression under control of the arabinose promoter Plasmid: pB22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 References: UniProt: P32722, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | ChemComp-C8E / ( |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4 Details: 0.1 M LiSO4, 0.1 M NaCl, 0.1 M Na citrate, 28-32% PEG 400 (pH 3.5), pH 4.0, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2006 / 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: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 22385 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1872 / % possible all: 82.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.03 Å / Rfactor Rfree error: 0.032
|