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Yorodumi- PDB-7jx9: The crystal structure of human ornithine aminotransferase with an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jx9 | ||||||
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Title | The crystal structure of human ornithine aminotransferase with an intermediate bound during inactivation by (1S,3S)-3-amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid. | ||||||
Components | Ornithine aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / ornithine / aminotransferase / PLP / mechanism-based inactivator / intermediate / irreversible inhibitor / TRANSFERASE / 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: 1.96 Å | ||||||
Authors | Butrin, A. / Beaupre, B. / Shen, S. / Silverman, R.B. / Moran, G. / Liu, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Structural and Kinetic Analyses Reveal the Dual Inhibition Modes of Ornithine Aminotransferase by (1 S ,3 S )-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic Acid (BCF 3 ). Authors: Butrin, A. / Beaupre, B.A. / Kadamandla, N. / Zhao, P. / Shen, S. / Silverman, R.B. / Moran, G.R. / Liu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jx9.cif.gz | 261.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jx9.ent.gz | 209 KB | Display | PDB format |
PDBx/mmJSON format | 7jx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jx9_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7jx9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7jx9_validation.xml.gz | 51.9 KB | Display | |
Data in CIF | 7jx9_validation.cif.gz | 73.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/7jx9 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/7jx9 | HTTPS FTP |
-Related structure data
Related structure data | 1oatS S: Starting model for refinement |
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Similar structure data |
-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: Chemical | #4: 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: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 10% PEG 6000, 100 mM NaCl, and 10% glycerol, Tricine 100 mM, pH 7.8 |
-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: 1.1271 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.958→87.919 Å / Num. obs: 102687 / % possible obs: 99.6 % / Redundancy: 9.946 % / Biso Wilson estimate: 31.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.062 / Rrim(I) all: 0.196 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.958→1.991 Å / Redundancy: 7.854 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4891 / CC1/2: 0.381 / Rpim(I) all: 0.686 / Rrim(I) all: 1.98 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OAT Resolution: 1.96→48.21 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.75 / Stereochemistry target values: ML
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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 max: 89.82 Å2 / Biso mean: 34.9437 Å2 / Biso min: 14.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.96→48.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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