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- PDB-1c9c: ASPARTATE AMINOTRANSFERASE COMPLEXED WITH C3-PYRIDOXAL-5'-PHOSPHATE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c9c | ||||||
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Title | ASPARTATE AMINOTRANSFERASE COMPLEXED WITH C3-PYRIDOXAL-5'-PHOSPHATE | ||||||
![]() | ASPARTATE AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE / ENZYME-SUBSTRATE COMPLEX | ||||||
Function / homology | ![]() L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Ishijima, J. / Nakai, T. / Kawaguchi, S. / Hirotsu, K. / Kuramitsu, S. | ||||||
![]() | ![]() Title: Free energy requirement for domain movement of an enzyme Authors: Ishijima, J. / Nakai, T. / Kawaguchi, S. / Hirotsu, K. / Kuramitsu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.1 KB | Display | ![]() |
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PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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 | THE FUNCTIONAL DIMER CAN BE GENERATED BY APPLYING THE SYMMETRY OPERATOR (X, -Y, -Z) TO THE ATOMIC COORDINATES PRESENTED IN THIS ENTRY. |
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Components
#1: Protein | Mass: 43619.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PP3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.69 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, potassium phosphate, C3-pyridoxal-5p-phosphate, sodium azide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 104038 / Num. obs: 19863 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.22 / Num. unique all: 1947 / % possible all: 90.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 77327 |
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Processing
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Refinement | Resolution: 2.4→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.202 / Rfactor Rfree: 0.271 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |