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- PDB-3mz0: Crystal structure of apo myo-inositol dehydrogenase from Bacillus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mz0 | ||||||
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Title | Crystal structure of apo myo-inositol dehydrogenase from Bacillus subtilis | ||||||
![]() | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / myo-inositol dehydrogenase / BsIDH | ||||||
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 | ![]() | 91.6 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 443.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nt2C ![]() 3nt4C ![]() 3nt5C ![]() 3ntoC ![]() 3ntqC ![]() 3ntrC C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38675.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 383 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.02 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 7.5 Details: 0.2M MgCl2, 0.1M HEPES pH 7.5, 30% PEG 400, microbatch, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2007 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97961 Å / Relative weight: 1 |
Reflection | Resolution: 1.539→19.7 Å / Num. obs: 60036 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.539→1.6 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 7.7 / Num. unique all: 5943 / Rsym value: 0.231 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: low resolution SeMet-IDH model Resolution: 1.539→19.696 Å / SU ML: 0.13 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 1.34 / Phase error: 18.48 / 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: 67.881 Å2 / ksol: 0.436 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.539→19.696 Å
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Refine LS restraints |
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LS refinement shell |
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