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Yorodumi- PDB-5ofy: Crystal structure of the D183N variant of human Alanine:Glyoxylat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ofy | ||||||
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Title | Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; 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: 2.8 Å | ||||||
Authors | Giardina, G. / Cutruzzola, F. / Borri Voltattorni, C. / Cellini, B. / Montioli, R. | ||||||
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 | 5ofy.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ofy.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ofy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/5ofy ftp://data.pdbj.org/pub/pdb/validation_reports/of/5ofy | HTTPS FTP |
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-Related structure data
Related structure data | 5f9sC 5hhyC 5lucSC 5og0C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43061.852 Da / Num. of mol.: 1 / Mutation: D183N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Production host: Escherichia coli (E. coli) References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-DIO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 Details: protein - 15 mg/ml (165 microM) in 40 mM PhO pH 7.4, 60 mM Hepes pH 7.0, 1.6 molar excess PLP Reservoir - Hampton Research Crystal Screen solution H12 - 2% dioxane, 0.1M bicine pH 9.0, 10% ...Details: protein - 15 mg/ml (165 microM) in 40 mM PhO pH 7.4, 60 mM Hepes pH 7.0, 1.6 molar excess PLP Reservoir - Hampton Research Crystal Screen solution H12 - 2% dioxane, 0.1M bicine pH 9.0, 10% PEG 20K Mixing - 0.4 + 0.4 microL PH range: 7.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.8→46.95 Å / Num. obs: 14614 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.026 / Rrim(I) all: 0.091 / Net I/σ(I): 20.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.512
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LUC Resolution: 2.8→46 Å / SU B: 26.913 / SU ML: 0.456 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.923 / ESU R Free: 0.429 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Displacement parameters | Biso mean: 89.86 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→46 Å
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