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- PDB-3blv: Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulato... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3blv | ||||||
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Title | Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits | ||||||
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![]() | OXIDOREDUCTASE / TCA cycle / oxidative metabolism / allostery / dehydrogenase / decarboxylase / Allosteric enzyme / Magnesium / Manganese / Metal-binding / Mitochondrion / NAD / RNA-binding / Transit peptide / Tricarboxylic acid cycle / Phosphoprotein | ||||||
Function / homology | ![]() isocitrate dehydrogenase complex (NAD+) / Citric acid cycle (TCA cycle) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / glutamate biosynthetic process / isocitrate metabolic process / mitochondrial nucleoid / tricarboxylic acid cycle / mitochondrial intermembrane space / NAD binding ...isocitrate dehydrogenase complex (NAD+) / Citric acid cycle (TCA cycle) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / glutamate biosynthetic process / isocitrate metabolic process / mitochondrial nucleoid / tricarboxylic acid cycle / mitochondrial intermembrane space / NAD binding / mitochondrial matrix / magnesium ion binding / mitochondrion / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Taylor, A.B. / Hu, G. / Hart, P.J. / McAlister-Henn, L. | ||||||
![]() | ![]() Title: Allosteric Motions in Structures of Yeast NAD+-specific Isocitrate Dehydrogenase. Authors: Taylor, A.B. / Hu, G. / Hart, P.J. / McAlister-Henn, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 511.4 KB | Display | ![]() |
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PDB format | ![]() | 422.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3blwC ![]() 3blxC ![]() 1wpwS 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39095.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: IDH1 / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: P28834, isocitrate dehydrogenase (NAD+) #2: Protein | Mass: 37979.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: IDH2 / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: P28241, isocitrate dehydrogenase (NAD+) #3: Chemical | ChemComp-FLC / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.56 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 1.1 M sodium citrate, 0.1 M CHES, 15% ethylene glycol, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2003 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→50 Å / Num. obs: 109531 / % possible obs: 96.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 68.6 Å2 / Rsym value: 0.101 / Net I/σ(I): 11 | |||||||||
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 11104 / Rsym value: 0.556 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: PDB entry 1WPW Resolution: 3.2→49.346 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
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Displacement parameters | Biso mean: 73.9 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→49.346 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.2364 Å
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