[English] 日本語
![](img/lk-miru.gif)
- PDB-5ofy: Crystal structure of the D183N variant of human Alanine:Glyoxylat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ofy | ||||||
---|---|---|---|---|---|---|---|
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 | ||||||
![]() | 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 / 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. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465.5 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f9sC ![]() 5hhyC ![]() 5lucSC ![]() 5og0C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 43061.852 Da / Num. of mol.: 1 / 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-DIO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.86 % |
---|---|
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
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
|
-Phasing
Phasing | Method: ![]() | ||||||
---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.512
|
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||
Displacement parameters | Biso mean: 89.86 Å2
| ||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→46 Å
|