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Yorodumi- PDB-3blw: Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3blw | ||||||
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Title | Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits | ||||||
Components |
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Keywords | 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 | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å | ||||||
Authors | Taylor, A.B. / Hu, G. / Hart, P.J. / McAlister-Henn, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3blw.cif.gz | 892.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3blw.ent.gz | 753.5 KB | Display | PDB format |
PDBx/mmJSON format | 3blw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3blw_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3blw_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 3blw_validation.xml.gz | 218 KB | Display | |
Data in CIF | 3blw_validation.cif.gz | 280.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3blw ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blw | HTTPS FTP |
-Related structure data
Related structure data | 3blvSC 3blxC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38076.352 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: IDH1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P28834, isocitrate dehydrogenase (NAD+) #2: Protein | Mass: 37839.027 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: IDH2 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P28241, isocitrate dehydrogenase (NAD+) #3: Chemical | ChemComp-FLC / #4: Chemical | ChemComp-AMP / |
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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: 3.06 Å3/Da / Density % sol: 59.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 18% polyethylene glycol 3350, 0.2 M potassium sulfate, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.3→50 Å / Num. obs: 44752 / % possible obs: 90.1 % / Redundancy: 3.2 % / Rsym value: 0.13 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 4.3→4.45 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3303 / Rsym value: 0.334 / % possible all: 66.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BLV Resolution: 4.3→49.383 Å / Isotropic thermal model: grouped isotropic / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 190.8 Å2
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Refinement step | Cycle: LAST / Resolution: 4.3→49.383 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.3→4.3936 Å
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