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- PDB-8onl: 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: 8onl | ||||||
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Title | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A | ||||||
![]() | Aminotransferase class IV | ||||||
![]() | TRANSFERASE / DAAT / Transaminase / point mutant / aminotransferase | ||||||
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 | ![]() | 126.5 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986.1 KB | Display | ![]() |
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Full document | ![]() | 988.1 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ayjC ![]() 8onjC ![]() 8onnC 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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Unit cell |
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Components
#1: Protein | Mass: 30918.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M NaNitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.74503 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.97 Å / Num. obs: 43170 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.052 / Rrim(I) all: 0.122 / Χ2: 0.98 / Net I/σ(I): 10.4 / Num. measured all: 232841 |
Reflection shell | Resolution: 1.9→1.94 Å / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.69 / Num. measured all: 15179 / Num. unique obs: 2747 / CC1/2: 0.731 / Rpim(I) all: 0.321 / Rrim(I) all: 0.763 / Χ2: 0.9 / Net I/σ(I) obs: 2.5 |
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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: 26.428 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→33.7 Å
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Refine LS restraints |
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