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Yorodumi- PDB-1ohy: 4-AMINOBUTYRATE-AMINOTRANSFERASE inactivated by gamma-ethynyl GABA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ohy | ||||||
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Title | 4-AMINOBUTYRATE-AMINOTRANSFERASE inactivated by gamma-ethynyl GABA | ||||||
Components | 4-AMINOBUTYRATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / PLP-DEPENDENT ENZYME / AMINOTRANSFERASE / 4- AMINOBUTYRIC ACID / ANTIEPILEPTIC DRUG TARGET / VIGABATRIN PYRIDOXAL PHOSPHATE / NEUROTRANSMITTER DEGRADATION / MITOCHONDRION / TRANSIT PEPTIDE | ||||||
Function / homology | Function and homology information (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / behavioral response to cocaine ...(S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / behavioral response to cocaine / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å | ||||||
Authors | Storici, P. / Schirmer, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structures of {Gamma}-Aminobutyric Acid (Gaba) Aminotransferase, a Pyridoxal 5'-Phosphate, and [2Fe-2S] Cluster-Containing Enzyme, Complexed with {Gamma}-Ethynyl-Gaba and with the Antiepilepsy Drug Vigabatrin Authors: Storici, P. / De Biase, D. / Bossa, F. / Bruno, S. / Mozzarelli, A. / Peneff, C. / Silverman, R. / Schirmer, T. #1: Journal: Biochemistry / Year: 1999 Title: Crystal Structure of Gaba-Aminotransferase, a Target for Antiepileptic Drug Therapy Authors: Storici, P. / Capitani, G. / De Biase, D. / Moser, M. / John, R.A. / Jansonius, J.N. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ohy.cif.gz | 338.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ohy.ent.gz | 283.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ohy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1ohy ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1ohy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 53368.996 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: AFTER REACTION WITH 4-AMINO-5-HEXYNOIC ACID (GEG)(GAMMA-ETHYNYL GABA) THE FRAGMENT GEG HAS BEEN GENERATED WHICH IS COVALENTLY ATTACHED VIA A DOUBLE BOND TO C4A OF PLP AND VIA A SINGLE BOND ...Details: AFTER REACTION WITH 4-AMINO-5-HEXYNOIC ACID (GEG)(GAMMA-ETHYNYL GABA) THE FRAGMENT GEG HAS BEEN GENERATED WHICH IS COVALENTLY ATTACHED VIA A DOUBLE BOND TO C4A OF PLP AND VIA A SINGLE BOND TO NZ OF THE ACTIVE SITE LYS 329 Source: (natural) SUS SCROFA (pig) / Organ: LIVER References: UniProt: P80147, 4-aminobutyrate-2-oxoglutarate transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-GEG / ( #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: 4-AMINOBUTAN | |
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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: 2.44 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.7 / Details: pH 5.70 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 42804 / % possible obs: 85.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.6199 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.47 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.44 / % possible all: 78.9 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 42802 / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.41 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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