[English] 日本語
Yorodumi- PDB-7d7q: Crystal structure of the transmembrane domain and linker region o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d7q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase | ||||||
Components | Phosphodiesterase | ||||||
Keywords | MEMBRANE PROTEIN / microbial rhodopsin / eight-transmembrane / light-dependent phosphodiesterase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / 3',5'-cyclic-nucleotide phosphodiesterase activity / signal transduction / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Salpingoeca rosetta (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Ikuta, T. / Shihoya, W. / Yamashita, K. / Nureki, O. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural insights into the mechanism of rhodopsin phosphodiesterase. Authors: Ikuta, T. / Shihoya, W. / Sugiura, M. / Yoshida, K. / Watari, M. / Tokano, T. / Yamashita, K. / Katayama, K. / Tsunoda, S.P. / Uchihashi, T. / Kandori, H. / Nureki, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7d7q.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7d7q.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 7d7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/7d7q ftp://data.pdbj.org/pub/pdb/validation_reports/d7/7d7q | HTTPS FTP |
---|
-Related structure data
Related structure data | 7cj3SC 7d7pC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4080668 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39263.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salpingoeca rosetta (strain ATCC 50818 / BSB-021) (eukaryote) Gene: PTSG_02023 / Production host: Homo sapiens (human) References: UniProt: F2TZN0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | #3: Chemical | ChemComp-OLC / ( Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 25% (w/v) PEG 500DME, 100mM Na-citrate, pH 5.0, 100mM NaK-tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→49.4 Å / Num. obs: 13712 / % possible obs: 98.1 % / Redundancy: 6.55 % / Biso Wilson estimate: 49.61 Å2 / CC1/2: 0.934 / Rrim(I) all: 0.673 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 3.5→3.71 Å / Num. unique obs: 2147 / CC1/2: 0.393 / Rrim(I) all: 2.868 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CJ3 Resolution: 3.5→49.4 Å / SU ML: 0.4813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3612 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→49.4 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|