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- PDB-7d7q: Crystal structure of the transmembrane domain and linker region o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d7q | ||||||
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Title | Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase | ||||||
![]() | Phosphodiesterase | ||||||
![]() | MEMBRANE PROTEIN / microbial rhodopsin / eight-transmembrane / light-dependent phosphodiesterase | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / regulation of signal transduction / 3',5'-cyclic-AMP phosphodiesterase activity / perinuclear region of cytoplasm / signal transduction / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ikuta, T. / Shihoya, W. / Yamashita, K. / Nureki, O. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.6 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cj3SC ![]() 7d7pC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39263.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PTSG_02023 / Production host: ![]() References: UniProt: F2TZN0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | #3: Chemical | ChemComp-OLC / ( Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.09 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refine LS restraints |
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LS refinement shell |
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