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Yorodumi- PDB-3mar: Crystal structure of homodimeric R132H mutant of human cytosolic ... -
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-Basic information
Entry | Database: PDB / ID: 3mar | ||||||
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Title | Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP | ||||||
Components | Isocitrate dehydrogenase [NADP] cytoplasmic | ||||||
Keywords | OXIDOREDUCTASE / isocitrate dehydrogenase / nicotinamide adenine dinucleotide phosphate / Rossmann fold | ||||||
Function / homology | Function and homology information Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / 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 / regulation of phospholipid catabolic process / NADPH regeneration / 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 / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / tertiary granule lumen / peroxisome / 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: 3.41 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 | 3mar.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mar.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3mar ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3mar | HTTPS FTP |
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-Related structure data
Related structure data | 3mapC 3masC 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.: 2 / 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+) #2: Chemical | |
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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: 2.83 Å3/Da / Density % sol: 56.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1.0M Na2HPO4/KH2PO4, pH 8.2, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 14215 / % possible obs: 91.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.561 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T09 Resolution: 3.41→50 Å / SU B: 36.264 / SU ML: 0.553 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.746 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.41→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.52 Å / Total num. of bins used: 10
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