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Yorodumi- PDB-7d7p: Crystal structure of the phosphodiesterase domain of Salpingoeca ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d7p | ||||||
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Title | Crystal structure of the phosphodiesterase domain 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 / 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 | Salpingoeca rosetta (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d7p.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d7p.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 7d7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d7p_validation.pdf.gz | 634.1 KB | Display | wwPDB validaton report |
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Full document | 7d7p_full_validation.pdf.gz | 636.6 KB | Display | |
Data in XML | 7d7p_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7d7p_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/7d7p ftp://data.pdbj.org/pub/pdb/validation_reports/d7/7d7p | HTTPS FTP |
-Related structure data
Related structure data | 7cj3C 7d7qC 5vydS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4080668 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42018.496 Da / Num. of mol.: 1 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 |
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-Non-polymers , 6 types, 183 molecules
#2: Chemical | ChemComp-2PE / | ||||||
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#3: Chemical | ChemComp-PEG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 29% (v/v) PEG 400, 50mM calcium acetate, pH 5.0, 200mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.53 Å / Num. obs: 22066 / % possible obs: 90.7 % / Redundancy: 11.6 % / CC1/2: 0.992 / Rrim(I) all: 0.162 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Num. unique obs: 1965 / CC1/2: 0.66 / Rrim(I) all: 0.798 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VYD Resolution: 2.1→47.516 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.516 Å
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Refine LS restraints |
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LS refinement shell |
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