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Yorodumi- PDB-1daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1daa | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE | ||||||
Components | D-AMINO ACID AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE (AMINOTRANSFERASE) / TRANSFERASE / AMINOTRANSFERASE / D-AMINO ACID / D-ALANINE / PYRIDOXAL PHOSPHATE | ||||||
Function / homology | Function and homology information D-amino acid biosynthetic process / D-alanine-2-oxoglutarate aminotransferase activity / D-amino-acid transaminase / D-amino acid catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.94 Å | ||||||
Authors | Sugio, S. / Peisach, D. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity. Authors: Sugio, S. / Petsko, G.A. / Manning, J.M. / Soda, K. / Ringe, D. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Kinetic and Stereochemical Comparison of Wild-Type and Active-Site K145Q Mutant Enzyme of Bacterial D-Amino Acid Transaminase Authors: Bhatia, M.B. / Futaki, S. / Ueno, H. / Manning, J.M. / Ringe, D. / Soda, K. #2: Journal: J.Biol.Chem. / Year: 1989 Title: Stereospecificity of Reactions Catalyzed by D-Amino Acid Amino-Transferase Authors: Martinez Del Pozo, A. / Merola, M. / Ueno, H. / Tanizawa, J.M.Manning K. / Nishimura, K. / Soda, K. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1daa.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1daa.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 1daa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1daa_validation.pdf.gz | 394.3 KB | Display | wwPDB validaton report |
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Full document | 1daa_full_validation.pdf.gz | 403.4 KB | Display | |
Data in XML | 1daa_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1daa_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1daa ftp://data.pdbj.org/pub/pdb/validation_reports/da/1daa | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32311.908 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / References: UniProt: P19938, D-amino-acid transaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: vapor diffusion, hanging drop / Details: Stoddard, B., (1987) J. Mol. Biol., 196, 441. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→99.9 Å / Num. obs: 40269 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.063 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 106545 / Rmerge(I) obs: 0.063 |
-Processing
Software |
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Refinement | Resolution: 1.94→10 Å / σ(F): 1
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Displacement parameters | Biso mean: 16.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→10 Å
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Refine LS restraints |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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