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- PDB-8ayj: 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: 8ayj | ||||||
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Title | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiens complexed with 3-aminooxypropionic acid | ||||||
![]() | Aminotransferase class IV | ||||||
![]() | TRANSFERASE / Transaminase / DAAT / aminotransferase / complex / oxyme / 3-aminooxypropionic acid / Aminobacterium colombiens | ||||||
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. / Nikolaeva, A.Y. / Shilova, S.A. / Rakitina, T.V. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
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 | ![]() | 135.2 KB | Display | ![]() |
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PDB format | ![]() | 103.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8onjC ![]() 8onlC ![]() 8onnC ![]() 8ahrS S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 0 - 275 / Label seq-ID: 2 - 277
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Components
#1: Protein | Mass: 30976.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-OCF / #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.02 M Sodium/potassium phosphate,0.1 M Bis-Tris propane pH 6.5, 20 % w/v 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 twin |
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Reflection | Resolution: 1.75→48.24 Å / Num. obs: 56226 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.109 / Rrim(I) all: 0.196 / Net I/σ(I): 4.3 / Num. measured all: 167509 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 95.4
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8AHR Resolution: 1.75→48.24 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2084 / WRfactor Rwork: 0.1741 / FOM work R set: 0.7596 / SU B: 4.219 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1373 / SU Rfree: 0.1299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 60.06 Å2 / Biso mean: 14.988 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 1.75→48.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8865 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.751→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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