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Yorodumi- PDB-8pny: Crystal structure of D-amino acid aminotransferase from Blastococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pny | |||||||||
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Title | Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens complexed with phenylhydrazine and in its apo form | |||||||||
Components | Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase | |||||||||
Keywords | TRANSFERASE / Aminotransferase / DAAT / apo form / transaminase / phenylhydrazine / complex | |||||||||
Function / homology | Function and homology information aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / L-valine biosynthetic process / lyase activity / cytosol Similarity search - Function | |||||||||
Biological species | Blastococcus saxobsidens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Matyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Popov, V.O. | |||||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens. Authors: Shilova, S.A. / Matyuta, I.O. / Petrova, E.S. / Nikolaeva, A.Y. / Rakitina, T.V. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y. #1: 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. #2: Journal: Int J Mol Sci / Year: 2023 Title: Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens Authors: Shilova, S.A. / Matyuta, I.O. / Petrova, E.S. / Nikolaeva, A.Y. / Rakitina, T.V. / 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 | 8pny.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pny.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pny_validation.pdf.gz | 747.7 KB | Display | wwPDB validaton report |
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Full document | 8pny_full_validation.pdf.gz | 749.7 KB | Display | |
Data in XML | 8pny_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8pny_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pny ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pny | HTTPS FTP |
-Related structure data
Related structure data | 8pnwC 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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-Components
#1: Protein | Mass: 29018.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastococcus saxobsidens (bacteria) / Gene: BLASA_4517 / Production host: Escherichia coli (E. coli) / References: UniProt: H6RQF3 |
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#2: Chemical | ChemComp-ZXN / [ |
#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: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.5, 4 M NaCl |
-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: Mar 31, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.59 Å / Num. obs: 30251 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.062 / Rrim(I) all: 0.224 / Χ2: 0.97 / Net I/σ(I): 10.7 / Num. measured all: 389046 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 96.6 % / Redundancy: 12.8 % / Rmerge(I) obs: 1.52 / Num. measured all: 22104 / Num. unique obs: 1727 / CC1/2: 0.506 / Rpim(I) all: 0.437 / Rrim(I) all: 1.583 / Χ2: 1.1 / Net I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.562 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.585 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→22.59 Å
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Refine LS restraints |
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