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- PDB-7d5m: Crystal structure of inositol dehydrogenase homolog complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d5m | ||||||
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Title | Crystal structure of inositol dehydrogenase homolog complexed with NAD+ from Azotobacter vinelandii | ||||||
![]() | Oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / Complex | ||||||
Function / homology | Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukano, K. / Ono, T. / Suzuki, M. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
![]() | ![]() Title: Crystal structure of inositol dehydrogenase complexed with NAD+ from Azotobacter vinelandii Authors: Fukano, K. / Ono, T. / Suzuki, M. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 71.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.5 KB | Display | ![]() |
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Full document | ![]() | 757 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dtyS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44131.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DJ / ATCC BAA-1303 / Gene: Avin_50260 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M ammonium tartrate dibasic, pH 7.0, 12% (w/v) PEG 3350, 10 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 46835 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 6 / Num. unique obs: 2284 / CC1/2: 0.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DTY Resolution: 1.75→37.663 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.843 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.094 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→37.663 Å
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Refine LS restraints |
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LS refinement shell |
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