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- PDB-1ry2: Crystal structure of yeast acetyl-coenzyme A synthetase in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ry2 | ||||||
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Title | Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP | ||||||
![]() | acetyl-coenzyme A synthetase 1 | ||||||
![]() | LIGASE / amp forming / related to firefly luciferase | ||||||
Function / homology | ![]() acetate fermentation / Ethanol oxidation / acid-ammonia (or amide) ligase activity / Transcriptional activation of mitochondrial biogenesis / : / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / acetyl-CoA biosynthetic process / AMP binding ...acetate fermentation / Ethanol oxidation / acid-ammonia (or amide) ligase activity / Transcriptional activation of mitochondrial biogenesis / : / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / acetyl-CoA biosynthetic process / AMP binding / endoplasmic reticulum / mitochondrion / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jogl, G. / Tong, L. | ||||||
![]() | ![]() Title: Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP Authors: Jogl, G. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.5 KB | Display | ![]() |
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PDB format | ![]() | 102.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761 KB | Display | ![]() |
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Full document | ![]() | 791.6 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pg4S 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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1 | ![]()
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Unit cell |
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Details | biological assembly is a trimer generated by space group symm -y, x-y, z -x+y, -x, z |
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Components
#1: Protein | Mass: 73603.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET28a / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-AMP / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: succinic acid, tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 271K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 21, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 27899 / Num. obs: 27899 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.9 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 79.1 |
Reflection | *PLUS Highest resolution: 2.3 Å / % possible obs: 89 % / Num. measured all: 85039 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 79 % / Rmerge(I) obs: 0.24 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1pg4 Resolution: 2.3→29.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 316294.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4283 Å2 / ksol: 0.306315 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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