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Yorodumi- PDB-7d5n: Crystal structure of inositol dehydrogenase homolog complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d5n | ||||||
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Title | Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii | ||||||
Components | Oxidoreductase | ||||||
Keywords | 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 / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Oxidoreductase Function and homology information | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fukano, K. / Ono, T. / Suzuki, M. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of inositol dehydrogenase complexed with NADH and myo-inositol 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d5n.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d5n.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/7d5n ftp://data.pdbj.org/pub/pdb/validation_reports/d5/7d5n | HTTPS FTP |
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-Related structure data
Related structure data | 3dtyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44458.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria) Strain: DJ / ATCC BAA-1303 / Gene: Avin_50260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1DLC3 #2: Chemical | #3: Chemical | ChemComp-INS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.04 Å3/Da / Density % sol: 39.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ca acetate, 14% PEG3350,10 mM NADH, 50 mM myo-inositol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 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: 1.8→50 Å / Num. obs: 63455 / % possible obs: 92.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2999 / CC1/2: 0.788 / % possible all: 59.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DTY Resolution: 1.8→48.166 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.679 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.12 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: 22.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.166 Å
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Refine LS restraints |
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LS refinement shell |
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