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- PDB-1yaa: ASPARTATE AMINOTRANSFERASE FROM SACCHAROMYCES CEREVISIAE CYTOPLASM -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yaa | ||||||
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Title | ASPARTATE AMINOTRANSFERASE FROM SACCHAROMYCES CEREVISIAE CYTOPLASM | ||||||
![]() | ASPARTATE AMINOTRANSFERASE | ||||||
![]() | AMINOTRANSFERASE / TRANSFERASE | ||||||
Function / homology | ![]() asparagine biosynthetic process from oxaloacetate / Aspartate and asparagine metabolism / Gluconeogenesis / aspartate metabolic process / aspartate biosynthetic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / peroxisome ...asparagine biosynthetic process from oxaloacetate / Aspartate and asparagine metabolism / Gluconeogenesis / aspartate metabolic process / aspartate biosynthetic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / peroxisome / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jeffery, C.J. | ||||||
![]() | ![]() Title: Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase. Authors: Jeffery, C.J. / Barry, T. / Doonan, S. / Petsko, G.A. / Ringe, D. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Aspartate Aminotransferase from Saccharomyces Cerevisiae Authors: Jeffery, C.J. / Barry, T. / Doonan, S. / Petsko, G.A. / Ringe, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.6 KB | Display | ![]() |
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PDB format | ![]() | 271.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.1 KB | Display | ![]() |
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Full document | ![]() | 448 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cstS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45361.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: PYRIDOXAL PHOSPHATE COFACTOR COVALENTLY BOUND TO LYS 258 VIA SCHIFF BASE LINKAGE IN EACH SUBUNIT Source: (natural) ![]() ![]() #2: Chemical | ChemComp-MAE / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: PROTEIN SOLUTION CONTAINED 5-15MG PROTEIN, 10MM PMSF, 10MM PLP, 10MM SODIUM ACETATE BUFFER, PH 5.8, AND 100MM MALEATE. RESERVOIR SOLUTION CONTAINED 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ...Details: PROTEIN SOLUTION CONTAINED 5-15MG PROTEIN, 10MM PMSF, 10MM PLP, 10MM SODIUM ACETATE BUFFER, PH 5.8, AND 100MM MALEATE. RESERVOIR SOLUTION CONTAINED 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE BUFFER, PH 4.6, AND 20-22% PEG 4000. PH range: 4.6-5.8 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.8 / Method: vapor diffusion, hanging drop / Details: Jeffery, C.J., (1998) Acta Cryst., D54, 659. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1992 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.05 Å / Num. obs: 470081 / % possible obs: 93 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 |
Reflection shell | Resolution: 2.05→2.14 Å / % possible all: 87 |
Reflection | *PLUS Num. obs: 100347 / % possible obs: 93 % / Num. measured all: 470081 |
Reflection shell | *PLUS % possible obs: 88 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CST Resolution: 2.05→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.14 Å / Rfactor Rfree error: 0.001 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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