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Yorodumi- PDB-3daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3daa | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE | ||||||
Components | D-AMINO ACID AMINOTRANSFERASE | ||||||
Keywords | AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / TRANSAMINASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Peisach, D. / Chipman, D.M. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase. Authors: Peisach, D. / Chipman, D.M. / Van Ophem, P.W. / Manning, J.M. / 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 | 3daa.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3daa.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 3daa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3daa_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3daa_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3daa_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3daa_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3daa ftp://data.pdbj.org/pub/pdb/validation_reports/da/3daa | HTTPS FTP |
-Related structure data
Related structure data | 4daaC 1daaS S: Starting model for refinement C: citing same article (ref.) |
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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: 31721.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / Production host: Escherichia coli (E. coli) / 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: 2.1 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: PDA INACTIVATED PROTEIN WAS 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 ...Details: PDA INACTIVATED PROTEIN WAS 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 27% PEG 4000, 0.3 M SODIUM ACETATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop PH range: 7.6-8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 14, 1996 / Details: MIRROR |
Radiation | Monochromator: FLAT CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 43763 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 2.47 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.5 / % possible all: 76.1 |
Reflection | *PLUS Num. measured all: 57553 |
Reflection shell | *PLUS % possible obs: 76.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAA Resolution: 1.9→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: USED SOLVENT MASK DURING REFINEMENT
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Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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