+Open data
-Basic information
Entry | Database: PDB / ID: 7q9q | ||||||
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Title | Crystal structure of PDE6D Geranylgeranylated cystein complex | ||||||
Components | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | ||||||
Keywords | TRANSPORT PROTEIN / Complex | ||||||
Function / homology | Function and homology information ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Yelland, T. / Ismail, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling. Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. ...Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. / Jamieson, A. / Chen, Y.X. / McArthur, D. / Bower, J. / Ismail, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q9q.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q9q.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/7q9q ftp://data.pdbj.org/pub/pdb/validation_reports/q9/7q9q | HTTPS FTP |
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-Related structure data
Related structure data | 7q9rC 7q9sC 7q9uC 7qf9C 7qjkC 5tb5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17730.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43924 | ||||||
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#2: Chemical | ChemComp-CMT / | ||||||
#3: Chemical | #4: Chemical | ChemComp-GER / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→34.971 Å / Num. obs: 24436 / % possible obs: 95.9 % / Redundancy: 3.5 % / CC1/2: 1 / Net I/σ(I): 17.98 |
Reflection shell | Resolution: 1.45→1.49 Å / Num. unique obs: 1715 / CC1/2: 0.669 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TB5 Resolution: 1.45→34.971 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.201 / SU B: 2.617 / SU ML: 0.096 / Average fsc free: 0.8 / Average fsc work: 0.8215 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.1 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→34.971 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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