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Yorodumi- PDB-5jj2: Crystal structure of the central domain of human AKAP18 gamma/del... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jj2 | |||||||||||||||
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Title | Crystal structure of the central domain of human AKAP18 gamma/delta in complex with malonate | |||||||||||||||
Components | A-kinase anchor protein 7 isoform gamma | |||||||||||||||
Keywords | HYDROLASE / AKAP / A-kinase anchoring / phospoesterase / malonate / complex / central domain | |||||||||||||||
Function / homology | Function and homology information regulation of protein kinase A signaling / protein kinase A binding / protein kinase A regulatory subunit binding / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission / nucleotide binding / protein kinase binding / protein-containing complex / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||||||||
Authors | Bjerregaard-Andersen, K. / Ostensen, E. / Scott, J.D. / Tasken, K. / Morth, J.P. | |||||||||||||||
Funding support | Denmark, Norway, United States, 4items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Malonate in the nucleotide-binding site traps human AKAP18 gamma / delta in a novel conformational state. Authors: Bjerregaard-Andersen, K. / stensen, E. / Scott, J.D. / Tasken, K. / Morth, J.P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jj2.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jj2.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/5jj2 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/5jj2 | HTTPS FTP |
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-Related structure data
Related structure data | 2vfyS S: Starting model for refinement |
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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: 24214.184 Da / Num. of mol.: 1 / Fragment: UNP residues 76-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKAP7, AKAP18 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q9P0M2 | ||
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#2: Chemical | ChemComp-MLI / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5 M Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 14, 2015 |
Radiation | Monochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→44.36 Å / Num. obs: 119131 / % possible obs: 99.3 % / Redundancy: 12.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.49 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VFY Resolution: 1.25→44.36 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→44.36 Å
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Refine LS restraints |
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LS refinement shell |
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