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Yorodumi- PDB-3ai2: The crystal structure of L-sorbose reductase from Gluconobacter f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ai2 | ||||||
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Title | The crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH | ||||||
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: 1.9 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 | 3ai2.cif.gz | 428.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ai2.ent.gz | 352.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ai2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3ai2 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3ai2 | HTTPS FTP |
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-Related structure data
Related structure data | 3ai1SC 3ai3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28351.529 Da / Num. of mol.: 8 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: Chemical | ChemComp-NDP / #3: 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: 2.08 Å3/Da / Density % sol: 40.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 5MM NADPH, 34% (W/V) PEG 400, 200MM CALCIUM ACETATE, 100MM SODIUM ACETATE TRIHYDRATE PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, temperature 293.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 146936 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AI1 Resolution: 1.9→19.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.414 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 19.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.67 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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