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- PDB-4f1m: Crystal Structure of the G1179S Roco4 Kinase Domain bound to AppC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f1m | ||||||
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Title | Crystal Structure of the G1179S Roco4 Kinase Domain bound to AppCp from D. discoideum. | ||||||
![]() | Serine/threonine-protein kinase roco4 | ||||||
![]() | Transferase / Signaling Protein / Protein Kinase / LRRK2 / ROCO / Kinase / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase | ||||||
Function / homology | ![]() sorocarp stalk development / Regulation of necroptotic cell death / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity ...sorocarp stalk development / Regulation of necroptotic cell death / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / GTP binding / signal transduction / mitochondrion / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gilsbach, B.K. / Vetter, I.R. / Wittinghofer, A. / Kortholt, A. | ||||||
![]() | ![]() Title: Roco kinase structures give insights into the mechanism of Parkinson disease-related leucine-rich-repeat kinase 2 mutations. Authors: Gilsbach, B.K. / Ho, F.Y. / Vetter, I.R. / van Haastert, P.J. / Wittinghofer, A. / Kortholt, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.9 KB | Display | ![]() |
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PDB format | ![]() | 99.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766.5 KB | Display | ![]() |
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Full document | ![]() | 774.2 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4f0fC ![]() 4f0gC ![]() 4f1oC ![]() 4f1tC ![]() 3dtcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32646.566 Da / Num. of mol.: 1 / Fragment: Roco4 Kinase Domain, UNP residues 1019-1292 / Mutation: G1179S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6XHB2, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ACP / |
#3: Chemical | ChemComp-BTB / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 0.1 M Bis- Tris, 0.2 M Na/K Tartrate; 11% PEG 3350, pH 8.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→41.95 Å / Num. obs: 20648 / % possible obs: 100 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.141 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 2.04→2.09 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.18 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DTC Resolution: 2.04→41.95 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.193 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 36.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→41.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.09 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.75 Å / Origin y: -2.9969 Å / Origin z: -21.6362 Å
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