+Open data
-Basic information
Entry | Database: PDB / ID: 5wdr | |||||||||
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Title | Choanoflagellate Salpingoeca rosetta Ras with GMP-PNP | |||||||||
Components | Ras proteinRas GTPase | |||||||||
Keywords | ONCOPROTEIN / HYDROLASE / small G-protein / GTPase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Salpingoeca rosetta (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Kondo, Y. / Gee, C.L. / Kuriyan, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2017 Title: Deconstruction of the Ras switching cycle through saturation mutagenesis. Authors: Bandaru, P. / Shah, N.H. / Bhattacharyya, M. / Barton, J.P. / Kondo, Y. / Cofsky, J.C. / Gee, C.L. / Chakraborty, A.K. / Kortemme, T. / Ranganathan, R. / Kuriyan, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wdr.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wdr.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 5wdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/5wdr ftp://data.pdbj.org/pub/pdb/validation_reports/wd/5wdr | HTTPS FTP |
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-Related structure data
Related structure data | 5wdoC 5wdpC 5wdqC 5wdsSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19507.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Gene: PTSG_05504 / Plasmid: pProEX HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2UBE5, small monomeric GTPase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15 % PEG8000, 100 mM Bis-Tris, pH 5.5, 200 mM magnesium acetate, 50 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2015 Details: Pt/Rh coated collimating and toroid focusing mirrors |
Radiation | Monochromator: Kohzu: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.7 Å / Num. obs: 40589 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.047 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1969 / CC1/2: 0.428 / Rpim(I) all: 0.557 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5WDS Resolution: 1.6→34.261 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→34.261 Å
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Refine LS restraints |
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LS refinement shell |
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