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Yorodumi- PDB-8gru: Crystal structure of a constitutively active mutant of the alpha ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gru | ||||||
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Title | Crystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ICT, NAD and Ca | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Isocitrate dehydrogenase / NAD-dependent IDH / assembly / allosteric regulation | ||||||
Function / homology | Function and homology information : / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix ...: / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.847 Å | ||||||
Authors | Sun, P. / Chen, X. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction. Authors: Chen, X. / Sun, P. / Liu, Y. / Shen, S. / Ma, T. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gru.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gru.ent.gz | 207.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gru_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8gru_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 8gru_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 8gru_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/8gru ftp://data.pdbj.org/pub/pdb/validation_reports/gr/8gru | HTTPS FTP |
-Related structure data
Related structure data | 8grbC 8grdC 8grgC 8grhC 8gs5C 6kdfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36625.125 Da / Num. of mol.: 2 / Mutation: Q139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P50213 #2: Protein | Mass: 39152.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3B / Production host: Escherichia coli (E. coli) / References: UniProt: O43837-2 #3: Chemical | ChemComp-NAD / #4: Chemical | #5: Chemical | 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: 2.95 Å3/Da / Density % sol: 58.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2 M sodium malonate (pH 6.0), 20% (w/v) PEG 3350, 40 mM ICT, 40 mM NAD and 5 mM Ca2+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.847→50 Å / Num. obs: 42112 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.068 / Rrim(I) all: 0.246 / Χ2: 0.665 / Net I/σ(I): 2.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KDF Resolution: 2.847→40.958 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.22 Å2 / Biso mean: 44.4995 Å2 / Biso min: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.847→40.958 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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