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Yorodumi- PDB-3ai1: The crystal structure of L-sorbose reductase from Gluconobacter f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ai1 | ||||||
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Title | The crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose reveals the structure bases of its catalytic mechanism and high substrate selectivity | ||||||
Components | NADPH-sorbose reductase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann-fold / NADPH-dependent reductase / short chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gluconobacter frateurii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Kubota, K. / Nagata, K. / Okai, M. / Miyazono, K. / Tanokura, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose Authors: Kubota, K. / Nagata, K. / Okai, M. / Miyazono, K. / Soemphol, W. / Ohtsuka, J. / Yamamura, A. / Saichana, N. / Toyama, H. / Matsushita, K. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ai1.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ai1.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ai1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3ai1 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3ai1 | HTTPS FTP |
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-Related structure data
Related structure data | 3ai2C 3ai3C 2ew8S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 28351.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter frateurii (bacteria) / Gene: sboA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A4PB64, EC: 1.1.1.289 #2: 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: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 32% (w/v) PEG 2000, 100mM sodium acetate trihydrate pH 5.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 19391 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.094 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.38→2.47 Å / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 5.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EW8 Resolution: 2.38→39.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.252 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.693 / ESU R Free: 0.297 / 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: 39.725 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→39.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.442 Å / Total num. of bins used: 20
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