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Yorodumi- PDB-4e3q: PMP-bound form of Aminotransferase crystal structure from Vibrio ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e3q | ||||||
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Title | PMP-bound form of Aminotransferase crystal structure from Vibrio fluvialis | ||||||
Components | Pyruvate transaminase | ||||||
Keywords | TRANSFERASE / aminotransferase | ||||||
Function / homology | Function and homology information organonitrogen compound metabolic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Vibrio fluvialis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Midelfort, K.S. / Kumar, R. / Han, S. / Karmilowicz, M.J. / McConnell, K. / Gehlhaar, D.K. / Mistry, A. / Chang, J.S. / Anderson, M. / Vilalobos, A. ...Midelfort, K.S. / Kumar, R. / Han, S. / Karmilowicz, M.J. / McConnell, K. / Gehlhaar, D.K. / Mistry, A. / Chang, J.S. / Anderson, M. / Vilalobos, A. / Minshull, J. / Govindarajan, S. / Wong, J.W. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2013 Title: Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin. Authors: Midelfort, K.S. / Kumar, R. / Han, S. / Karmilowicz, M.J. / McConnell, K. / Gehlhaar, D.K. / Mistry, A. / Chang, J.S. / Anderson, M. / Villalobos, A. / Minshull, J. / Govindarajan, S. / Wong, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e3q.cif.gz | 714.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e3q.ent.gz | 611.9 KB | Display | PDB format |
PDBx/mmJSON format | 4e3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/4e3q ftp://data.pdbj.org/pub/pdb/validation_reports/e3/4e3q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53061.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio fluvialis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: F2XBU9 |
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-Non-polymers , 5 types, 1308 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PMP / #6: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG8000, 0.2M Lithium Sulfate, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 1, 2010 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 144629 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.05 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.79 Å / Cor.coef. Fo:Fc: 0.9636 / Cor.coef. Fo:Fc free: 0.9533 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.201 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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