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Yorodumi- PDB-4tnb: Crystal Structure of G Protein-Coupled Receptor Kinase 5 in Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tnb | ||||||
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Title | Crystal Structure of G Protein-Coupled Receptor Kinase 5 in Complex with Sangivamycin | ||||||
Components | G protein-coupled receptor kinase 5 | ||||||
Keywords | SIGNALING PROTEIN / GRK5-Sangivamycin complex / GPCR Kinase / Kinase / inhibitor | ||||||
Function / homology | Function and homology information G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / fat cell differentiation / regulation of signal transduction / protein kinase C binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipid binding ...G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / fat cell differentiation / regulation of signal transduction / protein kinase C binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipid binding / Wnt signaling pathway / nuclear membrane / G alpha (s) signalling events / G alpha (q) signalling events / protein autophosphorylation / regulation of cell cycle / protein kinase activity / nuclear speck / G protein-coupled receptor signaling pathway / protein serine/threonine kinase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å | ||||||
Authors | Bhardwaj, A. / Komolov, K.E. / Benovic, J.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Atomic Structure of G Protein-Coupled Receptor Kinase 5 (GRK5) Reveals Distinct Structural Features Novel for GRKs. Authors: Komolov, K.E. / Bhardwaj, A. / Benovic, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tnb.cif.gz | 237.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tnb.ent.gz | 189.4 KB | Display | PDB format |
PDBx/mmJSON format | 4tnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tnb_validation.pdf.gz | 826.2 KB | Display | wwPDB validaton report |
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Full document | 4tnb_full_validation.pdf.gz | 832.2 KB | Display | |
Data in XML | 4tnb_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 4tnb_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/4tnb ftp://data.pdbj.org/pub/pdb/validation_reports/tn/4tnb | HTTPS FTP |
-Related structure data
Related structure data | 4tndC 3nynS C: citing same article (ref.) 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: 67942.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRK5, GPRK5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P34947, G-protein-coupled receptor kinase |
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#2: Chemical | ChemComp-SGV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 21% PEG 3350, 0.15 M Sodium Chloride, 0.1 M BIS-TRIS pH 5.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2013 / Details: Toroidal focusing mirror |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.113→47.567 Å / Num. obs: 28334 / % possible obs: 83.7 % / Redundancy: 3.6 % / Rsym value: 0.112 / Net I/σ(I): 12.64 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.34 / Rsym value: 0.426 / % possible all: 51.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NYN Resolution: 2.113→47.567 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.113→47.567 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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