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- PDB-7cj3: Crystal structure of the transmembrane domain of Salpingoeca rose... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cj3 | ||||||
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Title | Crystal structure of the transmembrane domain 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 | ![]() | 123.8 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d7pC ![]() 7d7qC ![]() 1m0mS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 50 - 309 / Label seq-ID: 19 - 278
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Components
#1: Protein | Mass: 32527.029 Da / Num. of mol.: 2 / Fragment: Transmembrane domain 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 / ( #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 29-35% (w/v) PEG400, 100 mM Na-citrate, pH 5.0, 100 mM KSCN and 10 mM ZnCl2 |
-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: Jun 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.16 Å / Num. obs: 18193 / % possible obs: 99.9 % / Redundancy: 62.4 % / CC1/2: 0.996 / Rrim(I) all: 0.845 / Net I/σ(I): 7.13 |
Reflection shell | Resolution: 2.6→2.76 Å / Num. unique obs: 2909 / CC1/2: 0.609 / Rrim(I) all: 1317.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M0M Resolution: 2.6→49.11 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.877 / SU B: 18.36 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.193 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→49.11 Å
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Refine LS restraints |
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