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Yorodumi- PDB-8ayk: Crystal structure of D-amino acid aminotrensferase from Aminobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ayk | ||||||
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Title | Crystal structure of D-amino acid aminotrensferase from Aminobacterium colombiense complexed with D-glutamate | ||||||
Components | Aminotransferase class IV | ||||||
Keywords | TRANSFERASE / Transaminase / DAAT / aminotransferase / complex / D-cycloserine | ||||||
Function / homology | Function and homology information aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Aminobacterium colombiense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Matyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Rakitina, T.V. / Minyaev, M.E. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Molecules / Year: 2023 Title: To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Authors: Shilova, S.A. / Khrenova, M.G. / Matyuta, I.O. / Nikolaeva, A.Y. / Rakitina, T.V. / Klyachko, N.L. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ayk.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ayk.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ayk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ayk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ayk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ayk_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 8ayk_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/8ayk ftp://data.pdbj.org/pub/pdb/validation_reports/ay/8ayk | HTTPS FTP |
-Related structure data
Related structure data | 8ahrSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 274 / Label seq-ID: 3 - 276
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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.) Aminobacterium colombiense (bacteria) / Strain: DSM 12261 / ALA-1 / Gene: Amico_1844 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EHC5 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.2M NaNitrate, 0.1M Bis-tris propane pH 6,5,20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 25, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→21.48 Å / Num. obs: 44299 / % possible obs: 98.8 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Net I/σ(I): 19.3 / Num. measured all: 477331 / Scaling rejects: 436 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8AHR Resolution: 1.9→21.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.355 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1731 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.138 / 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: 77.16 Å2 / Biso mean: 23.985 Å2 / Biso min: 1.48 Å2
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Refinement step | Cycle: final / Resolution: 1.9→21.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8552 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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