+Open data
-Basic information
Entry | Database: PDB / ID: 7ce3 | ||||||
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Title | Crystal structure of human IDH3 holoenzyme in APO form. | ||||||
Components |
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Keywords | OXIDOREDUCTASE / IDH3 / NAD-IDH / NAD dependent isocitrate dehydrogenase | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process ...isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / nucleolus / magnesium ion binding / mitochondrion / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.472 Å | ||||||
Authors | Sun, P.K. / Ding, J.P. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2020 Title: Structure and allosteric regulation of human NAD-dependent isocitrate dehydrogenase. Authors: Sun, P. / Liu, Y. / 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 | 7ce3.cif.gz | 261.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ce3.ent.gz | 205.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ce3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ce3_validation.pdf.gz | 475.8 KB | Display | wwPDB validaton report |
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Full document | 7ce3_full_validation.pdf.gz | 517.9 KB | Display | |
Data in XML | 7ce3_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 7ce3_validation.cif.gz | 69.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7ce3 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7ce3 | HTTPS FTP |
-Related structure data
Related structure data | 6kdyS 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: 39638.637 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: 39142.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3G / Production host: Escherichia coli (E. coli) / References: UniProt: P51553 #3: Protein | | Mass: 39978.984 Da / Num. of mol.: 1 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 |
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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: 3.93 Å3/Da / Density % sol: 68.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.05M NH4Cl, 0.05M Bis-Tris, pH 6.5, 30% pentaerythritol ethoxylate |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.47→50 Å / Num. obs: 32854 / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.025 / Rrim(I) all: 0.105 / Χ2: 0.965 / Net I/σ(I): 8.1 / Num. measured all: 585722 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KDY Resolution: 3.472→46.339 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.34 / 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: 162.05 Å2 / Biso mean: 56.0915 Å2 / Biso min: 6.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.472→46.339 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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