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Yorodumi- PDB-1zca: Crystal structure of G alpha 12 in complex with GDP, Mg2+ and AlF4- -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zca | ||||||
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Title | Crystal structure of G alpha 12 in complex with GDP, Mg2+ and AlF4- | ||||||
Components | G alpha i/12 | ||||||
Keywords | SIGNALING PROTEIN / GTP-binding / Lipoprotein / Membrane / Palmitate / Transducer | ||||||
Function / homology | Function and homology information D5 dopamine receptor binding / regulation of fibroblast migration / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / response to xenobiotic stimulus => GO:0009410 / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of vascular associated smooth muscle cell migration / regulation of TOR signaling / embryonic digit morphogenesis / negative regulation of vascular associated smooth muscle cell proliferation ...D5 dopamine receptor binding / regulation of fibroblast migration / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / response to xenobiotic stimulus => GO:0009410 / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of vascular associated smooth muscle cell migration / regulation of TOR signaling / embryonic digit morphogenesis / negative regulation of vascular associated smooth muscle cell proliferation / Rho protein signal transduction / lateral plasma membrane / G protein-coupled receptor binding / brush border membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / regulation of cell shape / in utero embryonic development / cell differentiation / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Nance, M.R. / Tesmer, J.J.G. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: A new approach to producing functional G alpha subunits yields the activated and deactivated structures of G alpha(12/13) proteins. Authors: Kreutz, B. / Yau, D.M. / Nance, M.R. / Tanabe, S. / Tesmer, J.J. / Kozasa, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zca.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zca.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/1zca ftp://data.pdbj.org/pub/pdb/validation_reports/zc/1zca | HTTPS FTP |
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-Related structure data
Related structure data | 1zcbSC 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: 41952.535 Da / Num. of mol.: 2 Fragment: N-terminal residues 1-28 of G alpha i followed by residues 49-379 of G alpha 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFastBacHTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P27600 #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: 2.3 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000 (14%), Sodium Citrate (100 mM), NaCl (50 mM), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2004 / Details: Si(111) double-crystal monochromator |
Radiation | Monochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.1 Å / Num. all: 15297 / Num. obs: 15297 / % possible obs: 88.7 % / Redundancy: 2.2 % / Rsym value: 0.102 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.67 / Num. unique all: 589 / Rsym value: 0.296 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZCB Resolution: 2.9→29.1 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.801 / SU B: 21.827 / SU ML: 0.402 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS refinement was utilizied.
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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: 38.436 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→29.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→2.976 Å / Total num. of bins used: 20
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