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Yorodumi- PDB-3mas: Crystal structure of heterodimeric R132H mutant of human cytosoli... -
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-Basic information
Entry | Database: PDB / ID: 3mas | ||||||
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Title | Crystal structure of heterodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate | ||||||
Components | (Isocitrate dehydrogenase [NADP] cytoplasmic) x 2 | ||||||
Keywords | OXIDOREDUCTASE / isocitrate dehydrogenase / nicotinamide adenine dinucleotide phosphate / Rossmann fold | ||||||
Function / homology | Function and homology information Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / glutathione metabolic process / tricarboxylic acid cycle / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Yang, B. / Peng, Y. / Ding, J. | ||||||
Citation | Journal: Cell Res. / Year: 2010 Title: Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H. Authors: Yang, B. / Zhong, C. / Peng, Y. / Lai, Z. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mas.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mas.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3mas ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3mas | HTTPS FTP |
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-Related structure data
Related structure data | 3mapC 3marC 1t09S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47772.316 Da / Num. of mol.: 1 / Mutation: R132H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O75874, isocitrate dehydrogenase (NADP+) | ||||
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#2: Protein | Mass: 47237.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O75874, isocitrate dehydrogenase (NADP+) | ||||
#3: Chemical | #4: Chemical | Sequence details | THE PROTEIN IS A HETERODIMERIC MUTANT, WITH ARG 132 MUTATED TO HIS 132 IN ONE SUBUNIT, WHILE THE ...THE PROTEIN IS A HETERODIME | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.89 % / Mosaicity: 0.534 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES-Na, 2% PEG 400, 2.0M (NH4)2SO4, pH 7.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 18264 / % possible obs: 96.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.114 / Χ2: 0.735 / Net I/σ(I): 5.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T09 Resolution: 3.2→49.547 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.12 / 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 / Bsol: 47.647 Å2 / ksol: 0.339 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.46 Å2 / Biso mean: 85.832 Å2 / Biso min: 67.14 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→49.547 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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