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Yorodumi- PDB-7tev: Human Ornithine Aminotransferase cocrystallized with its inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tev | |||||||||
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Title | Human Ornithine Aminotransferase cocrystallized with its inhibitor, (3S,4R)-3-amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylate | |||||||||
Components | Ornithine aminotransferase, mitochondrial | |||||||||
Keywords | TRANSFERASE/Inhibitor / Human Ornithine Aminotransferase / hOAT / OAT / mechanism-based inhibitor / MBI / irreversible inhibitor / inactivator / TRANSFERASE / TRANSFERASE-Inhibitor complex | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | |||||||||
Authors | Butrin, A. / Zhu, W. / Silverman, R. / Liu, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Rational Design, Synthesis, and Mechanism of (3 S ,4 R )-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human ...Title: Rational Design, Synthesis, and Mechanism of (3 S ,4 R )-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase. Authors: Zhu, W. / Butrin, A. / Melani, R.D. / Doubleday, P.F. / Ferreira, G.M. / Tavares, M.T. / Habeeb Mohammad, T.S. / Beaupre, B.A. / Kelleher, N.L. / Moran, G.R. / Liu, D. / Silverman, R.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tev.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tev.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tev_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7tev_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7tev_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 7tev_validation.cif.gz | 72.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/7tev ftp://data.pdbj.org/pub/pdb/validation_reports/te/7tev | HTTPS FTP |
-Related structure data
Related structure data | 7tedC 7tfpC 1oatS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 44860.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: After purification, hOAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. ...Details: After purification, hOAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.907→88.438 Å / Num. obs: 113351 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 34.48 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.907→1.94 Å / Num. unique obs: 5443 / CC1/2: 0.296 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OAT Resolution: 1.91→44.22 Å / SU ML: 0.3071 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1251 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: 23.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→44.22 Å
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Refine LS restraints |
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LS refinement shell |
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