+Open data
-Basic information
Entry | Database: PDB / ID: 5tot | ||||||
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Title | Crystal structure of AAT H143L:H189L double mutant | ||||||
Components | Aspartate aminotransferase, cytoplasmicAspartate transaminase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Aspartate and asparagine metabolism / phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process ...Aspartate and asparagine metabolism / phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / Gluconeogenesis / glutamate metabolic process / 2-oxoglutarate metabolic process / oxaloacetate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 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: 1.4 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tot.cif.gz | 191.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tot.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/5tot ftp://data.pdbj.org/pub/pdb/validation_reports/to/5tot | HTTPS FTP |
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-Related structure data
Related structure data | 5tonC 5toqSC 5torC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 46759.906 Da / Num. of mol.: 2 / Mutation: H143L:H189L 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 40 mM NaOAc, 2mM PLP, 8% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→31.02 Å / Num. obs: 174786 / % possible obs: 99.7 % / Redundancy: 6.2 % / Net I/σ(I): 10.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TOQ Resolution: 1.4→31.02 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.02 Å
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Refine LS restraints |
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LS refinement shell |
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