+Open data
-Basic information
Entry | Database: PDB / ID: 3a8u | ||||||
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Title | Crystal Structure of omega-Amino Acid:Pyruvate Aminotransferase | ||||||
Components | Omega-amino acid--pyruvate aminotransferase | ||||||
Keywords | TRANSFERASE / Large pleated sheet / transaminase / Aminotransferase / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information beta-alanine-pyruvate transaminase / beta-alanine-pyruvate transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 Å | ||||||
Authors | Watanabe, N. / Sakabe, N. / Sakabe, K. / Sasaki, K. | ||||||
Citation | Journal: to be published Title: Crystal Structure of omega-Amino Acid:Pyruvate Aminotransferase Authors: Watanabe, N. / Sakabe, N. / Sakabe, K. / Sasaki, K. #1: Journal: J.Biochem. / Year: 1989 Title: Crystal structure analysis of omega-amino acid:pyruvate aminotransferase with a newly developed Weissenberg camera and an imaging plate using synchrotron radiation Authors: Watanabe, N. / Sakabe, K. / Sakabe, N. / Higashi, T. / Sasaki, K. / Aibara, S. / Morita, Y. / Yonaha, K. / Toyama, S. / Fukutani, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a8u.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a8u.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/3a8u ftp://data.pdbj.org/pub/pdb/validation_reports/a8/3a8u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 48668.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) References: UniProt: P28269, beta-alanine-pyruvate transaminase |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 277 K / Method: dialysis / pH: 7.8 Details: 2.2M ammonium sulphate, 0.33M potassium phosphate buffer, pH 7.8, Dialysis, temperature 277K |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 12, 1995 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→55.9 Å / Num. all: 137549 / Num. obs: 135011 / % possible obs: 73.6 % / Redundancy: 13 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 0.26 / Num. unique all: 3274 / % possible all: 17.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.734 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.774 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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