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Yorodumi- PDB-5ax8: Recombinant expression, purification and preliminary crystallogra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ax8 | ||||||
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Title | Recombinant expression, purification and preliminary crystallographic studies of the mature form of human mitochondrial aspartate aminotransferase | ||||||
Components | Aspartate aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / aspartate aminotransferase / plasma membrane fatty acid binding protein / kynurenine aminotransferase-IV / three-dimensional structure | ||||||
Function / homology | Function and homology information 4-hydroxyproline catabolic process / Malate-aspartate shuttle / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / Degradation of cysteine and homocysteine / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate biosynthetic process / aspartate metabolic process ...4-hydroxyproline catabolic process / Malate-aspartate shuttle / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / Degradation of cysteine and homocysteine / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate biosynthetic process / aspartate metabolic process / Glyoxylate metabolism and glycine degradation / glutamate metabolic process / Aspartate and asparagine metabolism / Glutamate and glutamine metabolism / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / fatty acid transport / pyridoxal phosphate binding / response to ethanol / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.989 Å | ||||||
Authors | Jiang, X. / Wang, J. / Chang, H. / Zhou, Y. | ||||||
Citation | Journal: Biosci Trends / Year: 2016 Title: Recombinant expression, purification and crystallographic studies of the mature form of human mitochondrial aspartate aminotransferase Authors: Jiang, X. / Wang, J. / Chang, H. / Zhou, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ax8.cif.gz | 601.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ax8.ent.gz | 503.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ax8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ax8_validation.pdf.gz | 475.5 KB | Display | wwPDB validaton report |
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Full document | 5ax8_full_validation.pdf.gz | 560.2 KB | Display | |
Data in XML | 5ax8_validation.xml.gz | 64 KB | Display | |
Data in CIF | 5ax8_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5ax8 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5ax8 | HTTPS FTP |
-Related structure data
Related structure data | 3pdbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45583.086 Da / Num. of mol.: 4 / Fragment: UNP residues 40-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOT2 / Plasmid: pET22b-hmAspAT / Production host: Escherichia coli (E. coli) References: UniProt: P00505, aspartate transaminase, kynurenine-oxoglutarate transaminase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M HEPES pH 6.8, 25% (v/v) Jeffamine ED-2001 pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.989→50 Å / Num. obs: 30161 / % possible obs: 97.2 % / Redundancy: 1.9 % / Rsym value: 0.083 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.989→3.05 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.265 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PDB Resolution: 2.989→48.315 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 33.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.989→48.315 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.5849 Å / Origin y: -16.4266 Å / Origin z: -62.0946 Å
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Refinement TLS group | Selection details: all |