+Open data
-Basic information
Entry | Database: PDB / ID: 3wgb | ||||||
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Title | Crystal structure of aeromonas jandaei L-allo-threonine aldolase | ||||||
Components | L-allo-threonine aldolase | ||||||
Keywords | LYASE / PYRIDOXAL-5'-PHOSPHATE / threonine aldolase | ||||||
Function / homology | Function and homology information L-allo-threonine aldolase / L-allo-threonine aldolase activity / amino acid metabolic process Similarity search - Function | ||||||
Biological species | Aeromonas jandaei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Qin, H.M. / Imai, F.L. / Miyakawa, T. / Kataoka, M. / Okai, M. / Ohtsuka, J. / Hou, F. / Nagata, K. / Shimizu, S. / Tanokura, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: L-allo-Threonine aldolase with an H128Y/S292R mutation from Aeromonas jandaei DK-39 reveals the structural basis of changes in substrate stereoselectivity. Authors: Qin, H.M. / Imai, F.L. / Miyakawa, T. / Kataoka, M. / Kitamura, N. / Urano, N. / Mori, K. / Kawabata, H. / Okai, M. / Ohtsuka, J. / Hou, F. / Nagata, K. / Shimizu, S. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wgb.cif.gz | 247.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wgb.ent.gz | 201.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/3wgb ftp://data.pdbj.org/pub/pdb/validation_reports/wg/3wgb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36612.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas jandaei (bacteria) / Gene: LATA, ltaA / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: O07051, L-allo-threonine aldolase #2: Chemical | ChemComp-PLG / #3: Chemical | ChemComp-GLY / | #4: 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: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 45% MPD, 0.1M HEPES-NAOH (PH7.5), 0.2M AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 13, 2009 |
Radiation | Monochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→86.92 Å / Num. obs: 41738 / % possible obs: 99.3 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.59→2.63 Å / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.856 / SU B: 12.921 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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