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- PDB-5og0: Crystal structure of human Alanine:Glyoxylate Aminotransferase ma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5og0 | ||||||
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Title | Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 2.5 Angstrom; internal aldimine with PLP in the active site | ||||||
![]() | Serine--pyruvate aminotransferase | ||||||
![]() | TRANSFERASE / AMINOTRANSFERASE / DETOXIFICATION / LIVER | ||||||
Function / homology | ![]() oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glyoxylate metabolic process / glycine biosynthetic process, by transamination of glyoxylate / L-alanine catabolic process / serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / Glyoxylate metabolism and glycine degradation / L-serine metabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glyoxylate metabolic process / glycine biosynthetic process, by transamination of glyoxylate / L-alanine catabolic process / serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / Glyoxylate metabolism and glycine degradation / L-serine metabolic process / L-cysteine catabolic process / glyoxylate catabolic process / transaminase activity / amino acid binding / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / pyridoxal phosphate binding / peroxisome / intracellular membrane-bounded organelle / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Giardina, G. / Cutruzzola, F. / Borri Voltattorni, C. / Cellini, B. / Montioli, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5f9sSC ![]() 5hhyC ![]() 5lucC ![]() 5ofyC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43062.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop 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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
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: 2.5→47.46 Å / Num. obs: 21107 / % possible obs: 100 % / Redundancy: 17.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.028 / Rrim(I) all: 0.119 / Net I/σ(I): 19 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.41
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F9S Resolution: 2.5→45 Å / SU B: 13.713 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.292 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Displacement parameters | Biso mean: 54.61 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→45 Å
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