+Open data
-Basic information
Entry | Database: PDB / ID: 5toq | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of AAT | ||||||
Components | Aspartate aminotransferase, cytoplasmic | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Aspartate and asparagine metabolism / Malate-aspartate shuttle / glutamate catabolic process to aspartate / phosphatidylserine decarboxylase activity / : / cysteine transaminase / L-cysteine transaminase activity / glycerol biosynthetic process / aspartate catabolic process / aspartate biosynthetic process ...Aspartate and asparagine metabolism / Malate-aspartate shuttle / glutamate catabolic process to aspartate / phosphatidylserine decarboxylase activity / : / cysteine transaminase / L-cysteine transaminase activity / glycerol biosynthetic process / aspartate catabolic process / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Mueser, T.C. / Dajnowicz, S. / Kovalevsky, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5'-phosphate in aspartate aminotransferase. Authors: Dajnowicz, S. / Parks, J.M. / Hu, X. / Gesler, K. / Kovalevsky, A.Y. / Mueser, T.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5toq.cif.gz | 368.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5toq.ent.gz | 296.6 KB | Display | PDB format |
PDBx/mmJSON format | 5toq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5toq_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5toq_full_validation.pdf.gz | 470.4 KB | Display | |
Data in XML | 5toq_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 5toq_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/5toq ftp://data.pdbj.org/pub/pdb/validation_reports/to/5toq | HTTPS FTP |
-Related structure data
Related structure data | 5tonC 5torC 5totC 1ajrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46809.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: GOT1 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express References: UniProt: P00503, aspartate transaminase, cysteine transaminase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 40mM NaOAc, 2mM PLP, 8%PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30.15 Å / Num. obs: 279978 / % possible obs: 99.1 % / Redundancy: 4.9 % / Net I/σ(I): 12 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AJR Resolution: 1.2→29.831 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.39
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→29.831 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|