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Yorodumi- PDB-2daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2daa | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE | ||||||
Components | D-AMINO ACID AMINOTRANSFERASE | ||||||
Keywords | PYRIDOXAL PHOSPHATE / PYRIDOXAMINE / TRANSAMINASE / ANTIBIOTIC / SUICIDE SUBSTRATE / CYCLOSERINE / TRANSFERASE / AMINOTRANSFERASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Peisach, D. / Chipman, D.M. / Ringe, D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1998 Title: D-Cycloserine Inactivation of D-Amino Acid Aminotransferase Leads to a Stable Noncovalent Protein Complex with an Aromatic Cycloserine-Plp Derivative Authors: Peisach, D. / Chipman, D.M. / Van Ophem, P.W. / Manning, J.M. / Petsko, G.A. / Ringe, D. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2daa.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2daa.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 2daa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2daa_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2daa_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2daa_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 2daa_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/2daa ftp://data.pdbj.org/pub/pdb/validation_reports/da/2daa | HTTPS FTP |
-Related structure data
Related structure data | 1daaS S: Starting model for refinement |
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Similar structure data |
-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 Details: COMPLEXED WITH CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE / Source: (gene. exp.) Bacillus sp. (bacteria) / Description: THERMOPHILIC BACILLUS SP. / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: PROTEIN CONCENTRATED TO 30 MG/ ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 22- ...Details: PROTEIN CONCENTRATED TO 30 MG/ ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 22-26% PEG 4000, 0.2-0.3 M SODIUM ACETATE, 25 MM CYCLOSERINE AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop PH range: 7.6-8.5 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 14, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 36340 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2.47 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 83705 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAA Resolution: 2.1→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1 / Details: USED SOLVENT MASK DURING REFINEMENT
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Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.185 / Rfactor Rfree: 0.239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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