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Yorodumi- PDB-3c4z: Crystal structure of G protein coupled receptor kinase 1 bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4z | ||||||
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Title | Crystal structure of G protein coupled receptor kinase 1 bound to ADP and magnesium chloride at 1.84A | ||||||
Components | Rhodopsin kinase | ||||||
Keywords | TRANSFERASE / Ser/Thr kinase / RGS homology domain / G protein coupled receptor kinase / GRK / GRK1 / rhodopsin kinase / P-loop / autophosphorylation / ADP / ATP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Prenylation / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein autophosphorylation / signal transduction / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Singh, P. / Tesmer, J.J.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structures of rhodopsin kinase in different ligand states reveal key elements involved in G protein-coupled receptor kinase activation. Authors: Singh, P. / Wang, B. / Maeda, T. / Palczewski, K. / Tesmer, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c4z.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4z.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c4z_validation.pdf.gz | 786.1 KB | Display | wwPDB validaton report |
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Full document | 3c4z_full_validation.pdf.gz | 790.4 KB | Display | |
Data in XML | 3c4z_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 3c4z_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4z ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4z | HTTPS FTP |
-Related structure data
Related structure data | 3c4wSC 3c4xC 3c4yC 3c50C 3c51C 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: 61429.934 Da / Num. of mol.: 1 / Fragment: UNP residues 1-535 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ADP / | #5: 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: 2.37 Å3/Da / Density % sol: 48.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: PEG 6000, NaCl, glycerol, MES pH 6.25, ADP, magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 49154 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C4W Resolution: 1.84→19.47 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 5.686 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→19.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.887 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -13.784 Å / Origin y: -20.815 Å / Origin z: 22.332 Å
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Refinement TLS group |
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