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- PDB-4yb4: Crystal structure of homoisocitrate dehydrogenase from Thermus th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yb4 | ||||||
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Title | Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH | ||||||
![]() | Homoisocitrate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Homoisocitrate dehydrogenase Thermus thermophilus | ||||||
Function / homology | ![]() isocitrate-homoisocitrate dehydrogenase / homoisocitrate dehydrogenase activity / isocitrate dehydrogenase (NAD+) activity / lysine biosynthetic process via aminoadipic acid / isocitrate metabolic process / tricarboxylic acid cycle / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takahashi, K. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
![]() | ![]() Title: Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH Authors: Takahashi, K. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.1 KB | Display | ![]() |
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PDB format | ![]() | 229.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 58.4 KB | Display | |
Data in CIF | ![]() | 80.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1x0lS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35967.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 629 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/48Y.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/48Y.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-48Y / ( #4: Chemical | ChemComp-NAI / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl (pH 8.5), 1.5 M Ammonium sulfate, 12 % (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 66916 / % possible obs: 95.1 % / Observed criterion σ(F): 3.9 / Observed criterion σ(I): 3.9 / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 18.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X0L Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.489 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED GN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.805 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→50 Å
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Refine LS restraints |
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