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Yorodumi- PDB-8yrt: Crystal structure of D-amino acid transaminase from Haliscomenoba... -
+Open data
-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 | ||||||
Components | Aminotransferase class IV | ||||||
Keywords | TRANSFERASE / DAAT / holo form / transaminase / aminotransferase / D-amino acid | ||||||
Function / homology | Function and homology information carboxylic acid biosynthetic process / organonitrogen compound biosynthetic process / transaminase activity Similarity search - Function | ||||||
Biological species | Haliscomenobacter hydrossis DSM 1100 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Matyuta, I.O. / Bakunova, A.K. / Minyaev, M.E. / Popov, V.O. / Boyko, K.M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yrt.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yrt.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 8yrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/8yrt ftp://data.pdbj.org/pub/pdb/validation_reports/yr/8yrt | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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.) Haliscomenobacter hydrossis DSM 1100 (bacteria) Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0 |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.96 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.274 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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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