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- PDB-1akb: STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1akb | ||||||
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Title | STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE | ||||||
![]() | ASPARTATE AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE(AMINOTRANSFERASE) | ||||||
Function / homology | ![]() Amino acid metabolism / Gluconeogenesis / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity ...Amino acid metabolism / Gluconeogenesis / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Malashkevich, V.N. / Jansonius, J.N. | ||||||
![]() | ![]() Title: Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue. Authors: Malashkevich, V.N. / Jager, J. / Ziak, M. / Sauder, U. / Gehring, H. / Christen, P. / Jansonius, J.N. #1: ![]() Title: Mutant Aspartate Aminotransferase (K258H) without Pyridoxal-5'-Phosphate-Binding Lysine Residue. Structural and Catalytic Properties Authors: Ziak, M. / Jaeger, J. / Malashkevich, V.N. / Jaussi, R. / Gehring, H. / Jansonius, J.N. / Christen, P. #2: ![]() Title: Structural Basis for Catalysis by Aspartate Aminotransferase Authors: Jansonius, J.N. / Vincent, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.6 KB | Display | ![]() |
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PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195 3: K258H ACTIVE SITE MUTANT. THE RESIDUE PPD A 411 REPRESENTS THE COVALENT ADDUCT BETWEEN SUBSTRATE L-ASPARTATE AND PYRIDOXAL-5'-PHOSPHATE WITH THE REDUCED ALDIMINE BOND. |
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Components
#1: Protein | Mass: 45001.453 Da / Num. of mol.: 1 / Mutation: K250H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | ChemComp-PPD / | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | ONE MOLECULE OF N-(5'-PHOSPHOPYRSequence details | THE RESIDUES ARE NUMBERED FROM 3 - 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE LONGER SEQUENCE ...THE RESIDUES ARE NUMBERED FROM 3 - 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE LONGER SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: other | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. obs: 18825 / % possible obs: 96.2 % / Num. measured all: 72346 / Rmerge(I) obs: 0.082 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |