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- PDB-8onn: Crystal structure of D-amino acid aminotransferase from Aminobact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8onn | ||||||
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Title | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with 3-aminooxypropionic acid | ||||||
![]() | Aminotransferase class IV | ||||||
![]() | TRANSFERASE / DAAT / Transaminase / point mutant / aminotransferase / complex / 3-aminooxypropionic acid | ||||||
Function / homology | ![]() aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Matyuta, I.O. / Boyko, K.M. / Minyaev, M.E. / Shilova, S.A. / Bezsudnova, E.Y. / Popov, V.O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity. Authors: Shilova, S.A. / Matyuta, I.O. / Khrenova, M.G. / Nikolaeva, A.Y. / Klyachko, N.L. / Minyaev, M.E. / Khomutov, A.R. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 528.1 KB | Display | ![]() |
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PDB format | ![]() | 436.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 49.6 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ayjC ![]() 8onjC ![]() 8onlC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 30918.793 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-OCF / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75268 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.55 Å / Num. obs: 79705 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.063 / Rrim(I) all: 0.132 / Χ2: 0.92 / Net I/σ(I): 7.9 / Num. measured all: 333904 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible obs: 96.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.698 / Num. measured all: 18601 / Num. unique obs: 4502 / CC1/2: 0.658 / Rpim(I) all: 0.387 / Rrim(I) all: 0.8 / Χ2: 0.68 / Net I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.564 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→47.55 Å
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Refine LS restraints |
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