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Yorodumi- PDB-5f9s: Crystal structure of human Alanine:Glyoxylate Aminotransferase ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f9s | |||||||||
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Title | Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.7 Angstrom; internal aldimine with PLP in the active site | |||||||||
Components | Serine--pyruvate aminotransferase | |||||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / DETOXIFICATION / LIVER | |||||||||
Function / homology | Function and homology information oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process / glyoxylate catabolic process / Glyoxylate metabolism and glycine degradation / transaminase activity / amino acid binding / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / peroxisome / : / pyridoxal phosphate binding / intracellular membrane-bounded organelle / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | |||||||||
Authors | Giardina, G. / Cutruzzola, F. / Borri Voltattorni, C. / Cellini, B. / Montioli, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis. Authors: Giardina, G. / Paiardini, A. / Montioli, R. / Cellini, B. / Voltattorni, C.B. / Cutruzzola, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f9s.cif.gz | 305.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f9s.ent.gz | 251.4 KB | Display | PDB format |
PDBx/mmJSON format | 5f9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9s ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9s | HTTPS FTP |
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-Related structure data
Related structure data | 5hhyC 5lucC 5ofyC 5og0C 1hocS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42393.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Plasmid: pTRCHis2A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.47 % / Description: yellow plates |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein solution; 0.2 M AGT, 18mM potassium phosphate pH7.4, 20mM Hepes pH 7.4, 5% Jeffamine (Hampton), 5mM sodium hydroxylamine. Reservoir; PEG 6k 12%, 100 mM MES pH 5.0. Mixing: 1+1 microL ...Details: Protein solution; 0.2 M AGT, 18mM potassium phosphate pH7.4, 20mM Hepes pH 7.4, 5% Jeffamine (Hampton), 5mM sodium hydroxylamine. Reservoir; PEG 6k 12%, 100 mM MES pH 5.0. Mixing: 1+1 microL Cryoprotectant; 25% MPD PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 150 frames, osc. 0.75 degrees | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.7→48.04 Å / Num. obs: 70070 / % possible obs: 87 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.042 / Net I/σ(I): 10.6 / Num. measured all: 294083 / Scaling rejects: 113 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.552
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hoc Resolution: 1.7→45.118 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.27 / 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: 82.01 Å2 / Biso mean: 22.7206 Å2 / Biso min: 10.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→45.118 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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