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- PDB-8yrt: 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: 8yrt | ||||||
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Title | Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis in the holo form obtained at pH 7.0 | ||||||
![]() | Aminotransferase class IV | ||||||
![]() | TRANSFERASE / DAAT / holo 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 in the holo form obtained at pH 7.0 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 | ![]() | 75.2 KB | Display | ![]() |
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PDB format | ![]() | 54.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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 on special symmetry positions |
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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-PLP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % |
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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: May 30, 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→21.96 Å / Num. obs: 21090 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Χ2: 1.01 / Net I/σ(I): 23.7 / Num. measured all: 139425 |
Reflection shell | Resolution: 2→2.05 Å / % possible obs: 97.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.391 / Num. measured all: 9847 / Num. unique obs: 1484 / CC1/2: 0.926 / Rpim(I) all: 0.164 / Rrim(I) all: 0.425 / Χ2: 0.97 / Net I/σ(I) obs: 4.9 |
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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: 23.137 Å2
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Refinement step | Cycle: 1 / Resolution: 2→21.96 Å
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Refine LS restraints |
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