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Yorodumi- PDB-8pnx: Crystal structure of D-amino acid aminotransferase from Blastococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pnx | ||||||
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Title | Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in PMP form | ||||||
Components | Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase | ||||||
Keywords | TRANSFERASE / Aminotransferase / DAAT / PMP / transaminase | ||||||
Function / homology | Function and homology information aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / 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: To Be Published Title: Structural determinants of dual substrate recognition in the transaminase from Blastococcus saxobsidens specific to D-amino acids and R-amines Authors: Shilova, S.A. / Nikolaeva, A.Y. / Matyuta, I.O. / 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 | 8pnx.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pnx.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 8pnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pnx_validation.pdf.gz | 763.3 KB | Display | wwPDB validaton report |
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Full document | 8pnx_full_validation.pdf.gz | 764.4 KB | Display | |
Data in XML | 8pnx_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 8pnx_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnx ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnx | HTTPS FTP |
-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
#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-PMP / | ||||
#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | #5: 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: 2.83 Å3/Da / Density % sol: 56.51 % |
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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: Dec 20, 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: 1.8→20.55 Å / Num. obs: 30325 / % possible obs: 99.2 % / Redundancy: 15.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.028 / Rrim(I) all: 0.114 / Χ2: 0.94 / Net I/σ(I): 23.2 / Num. measured all: 481580 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 95.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.462 / Num. measured all: 21447 / Num. unique obs: 1744 / CC1/2: 0.836 / Rpim(I) all: 0.133 / Rrim(I) all: 0.482 / Χ2: 0.96 / Net I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.55 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 2.524 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / 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: 10.965 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→20.55 Å
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Refine LS restraints |
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