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Yorodumi- PDB-1aka: STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aka | ||||||
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Title | STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE | ||||||
Components | ASPARTATE AMINOTRANSFERASEAspartate transaminase | ||||||
Keywords | TRANSFERASE(AMINOTRANSFERASE) | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Malashkevich, V.N. / Jansonius, J.N. | ||||||
Citation | Journal: Biochemistry / Year: 1995 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: Journal: Eur.J.Biochem. / Year: 1993 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: Journal: Biological Macromolecules and Assemblies / Year: 1987 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aka.cif.gz | 183.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aka.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 1aka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1aka ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1aka | HTTPS FTP |
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-Related structure data
-Links
-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: CIS PROLINE - PRO B 138 / 4: CIS PROLINE - PRO B 195 5: K258H ACTIVE SITE MUTANT, PLP-FORM. THE RESIDUE PLP A 411 REPRESENTS THE COENZYME PLP IN THE ALDEHYDE FORM. IN SUBUNIT B, PLP IS REPLACED BY THE PHOSPHATE ION, PO4 B 411. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.923, 0.3525, -0.153), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 45001.453 Da / Num. of mol.: 2 / Mutation: K272H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Production host: unidentified (others) / References: UniProt: P00508, aspartate transaminase #2: Chemical | ChemComp-PLP / | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | COENZYME PYRIDOXAL-5'-PHOSPHATE IS BOUND (NON-COVALENTLY) IN SUBUNIT A, BUT IS REPLACED BY ...COENZYME PYRIDOXAL-5'-PHOSPHATE IS BOUND (NON-COVALENTLY | Sequence 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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: 2.1 Å / Lowest resolution: 10 Å / Num. obs: 41517 / % possible obs: 81.1 % / Num. measured all: 56002 / Rmerge(I) obs: 0.053 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 0.231 / Rfactor obs: 0.169 / Rfactor Rwork: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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