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Yorodumi- PDB-6kde: Crystal structure of the alpha beta heterodimer of human IDH3 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kde | ||||||
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Title | Crystal structure of the alpha beta heterodimer of human IDH3 in complex with Ca(2+) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NAD dependent isocitrate dehydrogenase | ||||||
Function / homology | Function and homology information : / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / NAD binding / electron transfer activity / carbohydrate metabolic process / mitochondrial matrix ...: / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / NAD binding / electron transfer activity / 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: 2.999 Å | ||||||
Authors | Sun, P. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Molecular basis for the function of the alpha beta heterodimer of human NAD-dependent isocitrate dehydrogenase. Authors: Sun, P. / Ma, T. / Zhang, T. / Zhu, H. / Zhang, J. / Liu, Y. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kde.cif.gz | 251.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kde.ent.gz | 198.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kde ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kde | HTTPS FTP |
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-Related structure data
Related structure data | 6kdfC 6kdyC 6ke3C 5grhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36826.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3A / Production host: Escherichia coli (E. coli) References: UniProt: P50213, isocitrate dehydrogenase (NAD+) #2: Protein | Mass: 39703.664 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 #3: Chemical | Has ligand of interest | Y | Sequence details | THIS SEQUENCE OF IDH3 B CORRESPOND | |
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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: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M calcium acetate (pH 7.5) and 20%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.999→50 Å / Num. obs: 34725 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.073 / Χ2: 0.531 / Net I/σ(I): 6.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GRH Resolution: 2.999→41.367 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.39 Å2 / Biso mean: 75.1623 Å2 / Biso min: 40.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.999→41.367 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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