[English] 日本語
Yorodumi- PDB-8qfj: Room temperature crystal structure of the Photoactivated Adenylat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qfj | ||||||
---|---|---|---|---|---|---|---|
Title | Room temperature crystal structure of the Photoactivated Adenylate Cyclase OaPAC after blue light excitation at 2.3 us delay | ||||||
Components | Family 3 adenylate cyclase | ||||||
Keywords | LYASE / Photoreceptor / BLUF / Adenylate Cyclase / PAC | ||||||
Function / homology | Function and homology information blue light photoreceptor activity / cAMP biosynthetic process / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Oscillatoria acuminata PCC 6304 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / C.P.Koliyadu, J. / Letrun, R. / Round, A. ...Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / C.P.Koliyadu, J. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R. / von Stetten, D. / Vakili, M. / Wrona, A. / Bean, R. / Mancuso, A. / Schulz, J. / R.Pearson, A. / Kottke, T. / Lorenzen, K. / Schubert, R. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: J.Mol.Biol. / Year: 2024 Title: Light-induced Trp in /Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. Authors: Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Dorner, K. / Han, H. / Koliyadu, J.C.P. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R.C. / von Stetten, ...Authors: Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Dorner, K. / Han, H. / Koliyadu, J.C.P. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R.C. / von Stetten, D. / Vakili, M. / Wrona, A. / Bean, R. / Mancuso, A. / Schulz, J. / Pearson, A.R. / Kottke, T. / Lorenzen, K. / Schubert, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qfj.cif.gz | 269.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qfj.ent.gz | 181.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qfj_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qfj_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8qfj_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 8qfj_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/8qfj ftp://data.pdbj.org/pub/pdb/validation_reports/qf/8qfj | HTTPS FTP |
-Related structure data
Related structure data | 8qfeC 8qffC 8qfgC 8qfhC 8qfiC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 39292.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oscillatoria acuminata PCC 6304 (bacteria) Gene: Oscil6304_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TLZ5 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-FMN / | ||||
#3: Chemical | ChemComp-ATP / | ||||
#4: Chemical | #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: 2.65 Å3/Da / Density % sol: 53.62 % |
---|---|
Crystal grow | Temperature: 277 K / Method: batch mode Details: 45% protein at 12 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 45% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine ...Details: 45% protein at 12 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 45% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine hydrochloride, 5 mM magnesium chloride 10% seeds from crushed macrocrystals |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3332 Å |
Detector | Type: AGIPD / Detector: PIXEL / Date: May 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3332 Å / Relative weight: 1 |
Reflection | Resolution: 1.815→31.63 Å / Num. obs: 37632 / % possible obs: 98.52 % / Redundancy: 936 % / Biso Wilson estimate: 30.5 Å2 / CC1/2: 0.988 / CC star: 0.997 / R split: 0.11 / Net I/σ(I): 1.3 |
Reflection shell | Resolution: 1.815→1.88 Å / Redundancy: 563 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3250 / CC1/2: 0.448 / CC star: 0.787 / % possible all: 86.37 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.63 Å / SU ML: 0.497 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 44.578 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: 45.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.63 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|