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- PDB-3pd6: Crystal structure of mouse mitochondrial aspartate aminotransfera... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pd6 | ||||||
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Title | Crystal structure of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV | ||||||
![]() | (Aspartate aminotransferase, ...) x 2 | ||||||
![]() | TRANSFERASE / alpha & beta protein / aminotransferase / PLP-binding / Mitochondrion | ||||||
Function / homology | ![]() Aspartate and asparagine metabolism / dicarboxylic acid metabolic process / Glutamate and glutamine metabolism / glutamate catabolic process to aspartate / Gluconeogenesis / glutamate catabolic process to 2-oxoglutarate / kynurenine-oxoglutarate transaminase / Glyoxylate metabolism and glycine degradation / kynurenine-oxoglutarate transaminase activity / aspartate biosynthetic process ...Aspartate and asparagine metabolism / dicarboxylic acid metabolic process / Glutamate and glutamine metabolism / glutamate catabolic process to aspartate / Gluconeogenesis / glutamate catabolic process to 2-oxoglutarate / kynurenine-oxoglutarate transaminase / Glyoxylate metabolism and glycine degradation / kynurenine-oxoglutarate transaminase activity / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / carboxylic acid binding / 2-oxoglutarate metabolic process / aspartate catabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / amino acid binding / fatty acid transport / T-tubule / phospholipid binding / sarcolemma / pyridoxal phosphate binding / myelin sheath / perikaryon / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / enzyme binding / cell surface / protein-containing complex / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J. | ||||||
![]() | ![]() Title: Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV. Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.1 KB | Display | ![]() |
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PDB format | ![]() | 273.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.2 KB | Display | ![]() |
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Full document | ![]() | 539.1 KB | Display | |
Data in XML | ![]() | 70.4 KB | Display | |
Data in CIF | ![]() | 98.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pdbC ![]() 3hlmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Aspartate aminotransferase, ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 44637.977 Da / Num. of mol.: 2 / Fragment: UNP residues 30-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 44866.094 Da / Num. of mol.: 2 / Fragment: UNP residues 30-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 847 molecules ![](data/chem/img/PMP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KYN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KYN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-KYN / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4000, 100mM ammonium sulphate, 6% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2007 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 76708 / Redundancy: 8.1 % / Rmerge(I) obs: 0.13 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HLM Resolution: 2.4→29.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.129 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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