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Yorodumi- PDB-3nt4: Crystal structure of myo-inositol dehydrogenase from Bacillus sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nt4 | ||||||
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Title | Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NADH and inositol | ||||||
Components | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / BSIDH / N-terminal Rossmann fold domain / glyceraldehyde-3-phosphate like C-terminal domain / cofactor NAD(H) / substrate inositol | ||||||
Function / homology | Function and homology information D-chiro-inositol 1-dehydrogenase / inositol 2-dehydrogenase / inositol 2-dehydrogenase (NAD+) activity / inositol catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5001 Å | ||||||
Authors | Van Straaten, K.E. / Palmer, D.R.J. / Sanders, D.A.R. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification. Authors: van Straaten, K.E. / Zheng, H. / Palmer, D.R. / Sanders, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nt4.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nt4.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 3nt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/3nt4 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/3nt4 | HTTPS FTP |
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-Related structure data
Related structure data | 3mz0SC 3nt2C 3nt5C 3ntoC 3ntqC 3ntrC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38394.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU39700, E83G, idh, iolG, NP_391849.2 / Plasmid: PHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: P26935, inositol 2-dehydrogenase #2: Chemical | #3: Chemical | #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: 3.4 Å3/Da / Density % sol: 63.83 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 5.4 Details: 0.2M di-sodium tartate, 2.2M ammonium sulfate, pH 5.4, microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 21, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→45.96 Å / Num. obs: 40387 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.14 % / Biso Wilson estimate: 76.2 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Χ2: 1 / Net I/σ(I): 12.7 / Scaling rejects: 5843 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MZ0 (apo-IDH) Resolution: 2.5001→33.661 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7038 / SU ML: 0.9 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.544 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.43 Å2 / Biso mean: 81.9898 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5001→33.661 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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