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- PDB-3ntr: Crystal structure of K97V mutant of myo-inositol dehydrogenase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ntr | ||||||
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Title | Crystal structure of K97V mutant of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NAD and inositol | ||||||
![]() | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / K97V mutant / BSIDH / N-terminal Rossmann fold domain / glyceraldehyde-3-phosphate like C-terminal domain | ||||||
Function / homology | ![]() D-chiro-inositol 1-dehydrogenase / inositol 2-dehydrogenase / inositol 2-dehydrogenase (NAD+) activity / inositol catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Van Straaten, K.E. / Palmer, D.R.J. / Sanders, D.A.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148 KB | Display | ![]() |
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PDB format | ![]() | 117 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 941.8 KB | Display | ![]() |
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Full document | ![]() | 961.7 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mz0C ![]() 3nt2SC ![]() 3nt4C ![]() 3nt5C ![]() 3ntoC ![]() 3ntqC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 38364.488 Da / Num. of mol.: 2 / Mutation: K97V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 5.4 Details: 0.1M tri-sodium citrate pH 5.4, 2M ammonium sulfate, microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 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: 2.65→19.81 Å / Num. obs: 29913 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.59 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.15 / Χ2: 0.96 / Net I/σ(I): 6.4 / Scaling rejects: 2394 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | % possible all: 100
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NT2 (holo-IDH) Resolution: 2.6503→19.808 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6463 / SU ML: 0.57 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.73 / 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: 48.636 Å2 / ksol: 0.27 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.76 Å2 / Biso mean: 102.8081 Å2 / Biso min: 46.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6503→19.808 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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