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- PDB-5luc: Crystal structure of the D183N variant of human Alanine:Glyoxylat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5luc | ||||||
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Title | Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site | ||||||
![]() | Serine--pyruvate aminotransferase | ||||||
![]() | TRANSFERASE / Primary Hyperoxaluria Type I / PH1 | ||||||
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 / L-serine metabolic process / L-cysteine catabolic 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Giardina, G. / Cutruzzola, F. / Cellini, B. / Borri Voltattorni, C. / 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 | ![]() | 690.1 KB | Display | ![]() |
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PDB format | ![]() | 560.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.6 KB | Display | ![]() |
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Full document | ![]() | 552.8 KB | Display | |
Data in XML | ![]() | 152 KB | Display | |
Data in CIF | ![]() | 230.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f9sSC ![]() 5hhyC ![]() 5ofyC ![]() 5og0C 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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Unit cell |
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Components
#1: Protein | Mass: 44280.152 Da / Num. of mol.: 8 / Mutation: D183N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-BTB / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.5 % / Description: Dimond shapes yellow xtals after 1 week |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: mixing equal volumes of protein solution: 15 mg/ml in 40 mM PhO pH 7.4 - 60 mM Hepes pH 7.0 reservoir: ammonium acetate o.1 M - BIS TRIS pH 5.5 0.1M - 17% PEG 10K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.8→57.23 Å / Num. obs: 397712 / % possible obs: 94.2 % / Redundancy: 4.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.2 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5f9s Resolution: 1.8→56.692 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.49 Å2 / Biso mean: 14.9516 Å2 / Biso min: 3.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→56.692 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: 30
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