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- PDB-4daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4daa | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM | ||||||
![]() | D-AMINO ACID AMINOTRANSFERASE | ||||||
![]() | AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / TRANSAMINASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Peisach, D. / Chipman, D.M. / Ringe, D. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3daaC ![]() 1daaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 100 MM 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 ...Details: PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 100 MM 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 25% PEG 4000, 200 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 1 MM ALPHA-KETOGLUTARATE, 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: 278 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 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: 2.25→30 Å / Num. obs: 31959 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 2.91 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.25→2.5 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.4 / % possible all: 69.5 |
Reflection | *PLUS Num. measured all: 92975 / Rmerge(I) obs: 0.149 |
Reflection shell | *PLUS % possible obs: 69.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DAA Resolution: 2.4→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: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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