+Open data
-Basic information
Entry | Database: PDB / ID: 9az7 | ||||||
---|---|---|---|---|---|---|---|
Title | Chloride Sites in Photoactive Yellow Protein | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / Photoreceptor / Light Sensor / Chromophore / Photoreceptor Protein / Receptor / Sensory Transduction / PAS / LOV | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | Halorhodospira halophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Dyda, F. / Schotte, F. / Anfinrud, P. / Cho, H.S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Struct Dyn. / Year: 2024 Title: Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein. Authors: Schotte, F. / Cho, H.S. / Dyda, F. / Anfinrud, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9az7.cif.gz | 50 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9az7.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 9az7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9az7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9az7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9az7_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 9az7_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/9az7 ftp://data.pdbj.org/pub/pdb/validation_reports/az/9az7 | HTTPS FTP |
-Related structure data
Related structure data | 9az9C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Plasmid: PET16B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16113 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-HC4 / | ||||
#3: Chemical | #4: 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: 1.9 Å3/Da / Density % sol: 35.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.2 M ammonium sulfate, 1.0 M sodium chloride, 20 mM sodium phosphate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 25, 2012 |
Radiation | Monochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→21.88 Å / Num. obs: 13007 / % possible obs: 94.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Net I/σ(I): 48.47 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.47 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 20 / Num. unique obs: 702 / CC1/2: 0.995 / % possible all: 67.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.88 Å / SU ML: 0.1448 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 18.3248 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→21.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|