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- PDB-8yru: Crystal structure of D-amino acid transaminase from Haliscomenoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yru | ||||||
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Title | Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine | ||||||
![]() | Aminotransferase class IV | ||||||
![]() | TRANSFERASE / DAAT / apo form / transaminase / aminotransferase / D-amino acid | ||||||
Function / homology | ![]() aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Matyuta, I.O. / Bakunova, A.K. / Minyaev, M.E. / Popov, V.O. / Boyko, K.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine Authors: Bakunova, A.K. / Matyuta, I.O. / Boyko, K.M. / Minyaev, M.E. / 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 | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 51.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 32321.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Halhy_2446 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-ZXN / [ |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 45% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0 |
-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: Jun 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→21.43 Å / Num. obs: 21346 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.092 / Χ2: 0.95 / Net I/σ(I): 16.8 / Num. measured all: 119567 |
Reflection shell | Resolution: 2→2.05 Å / % possible obs: 89.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.546 / Num. measured all: 6358 / Num. unique obs: 1390 / CC1/2: 0.824 / Rpim(I) all: 0.276 / Rrim(I) all: 0.615 / Χ2: 0.91 / Net I/σ(I) obs: 2.8 |
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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: 27.819 Å2
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Refinement step | Cycle: 1 / Resolution: 2→21.43 Å
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Refine LS restraints |
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