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- PDB-7ta0: Human Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ta0 | ||||||
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Title | Human Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleric acid | ||||||
![]() | Ornithine aminotransferase, mitochondrial | ||||||
![]() | TRANSFERASE / Human Ornithine Aminotransferase / hOAT / OAT / PLP / 5-aminovaleric acid / soaking | ||||||
Function / homology | ![]() arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Butrin, A. / Liu, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase. Authors: Butrin, A. / Butrin, A. / Wawrzak, Z. / Moran, G.R. / Liu, 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 | ![]() | 249.1 KB | Display | ![]() |
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PDB format | ![]() | 200.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 45.9 KB | Display | |
Data in CIF | ![]() | 63.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t9zC ![]() 7ta1C ![]() 1oatS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 48593.668 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion ...Details: Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 5-aminovaleric acid was added to the drop with crystals. The crystals were soaked for different time periods from 3 to 59 minutes. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.326→99.512 Å / Num. obs: 61264 / % possible obs: 99.9 % / Redundancy: 15.3 % / Biso Wilson estimate: 41.16 Å2 / CC1/2: 0.994 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.326→2.366 Å / Num. unique obs: 2995 / CC1/2: 0.33 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OAT Resolution: 2.33→99.51 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.964 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→99.51 Å
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Refine LS restraints |
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LS refinement shell |
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