[English] 日本語
Yorodumi- PDB-2oz6: Crystal Structure of Virulence Factor Regulator from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oz6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Virulence Factor Regulator from Pseudomonas aeruginosa in complex with cAMP | ||||||
Components | Virulence Factor Regulator | ||||||
Keywords | DNA BINDING PROTEIN / winged helix / helix-turn-helix / transcription factor / cAMP-binding proteins / cAMP Receptor Protein / nucleotide binding proteins / DNA-binding proteins | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cAMP binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Cordes, T.J. / Bright, A.R. / Forest, K.T. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2011 Title: Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator. Authors: Cordes, T.J. / Worzalla, G.A. / Ginster, A.M. / Forest, K.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2oz6.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2oz6.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 2oz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/2oz6 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/2oz6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1g6nS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23542.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAK / Gene: vfr / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) DELTA CRP / References: UniProt: P55222 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.9 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Sodium malonate, Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 | |||||||||
Detector | Type: BRUKER PROTEUM / Detector: CCD / Date: Jan 17, 2005 | |||||||||
Radiation | Monochromator: Montel 200 Multilayer Graded mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.8→32 Å / Num. obs: 8735 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 54 Å2 / Rsym value: 0.095 / Χ2: 1.026 / Net I/σ(I): 8.5 | |||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.79 / Num. unique all: 876 / Rsym value: 0.377 / Χ2: 0.881 / % possible all: 99.5 |
-Phasing
Phasing MR | Rfactor: 0.449 / Cor.coef. Fo:Fc: 0.492
|
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1G6N, chain A Resolution: 2.8→30 Å / FOM work R set: 0.812 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 35.926 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.832 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|