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Yorodumi- PDB-8gs5: Crystal structure of a constitutively active mutant of human IDH3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gs5 | ||||||
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Title | Crystal structure of a constitutively active mutant of human IDH3 holoenzyme in apo form | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Isocitrate dehydrogenase / NAD-dependent IDH / assembly / allosteric regulation | ||||||
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 / 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: 4.486 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 | 8gs5.cif.gz | 930.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gs5.ent.gz | 761.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gs5_validation.pdf.gz | 566.5 KB | Display | wwPDB validaton report |
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Full document | 8gs5_full_validation.pdf.gz | 767.9 KB | Display | |
Data in XML | 8gs5_validation.xml.gz | 203.5 KB | Display | |
Data in CIF | 8gs5_validation.cif.gz | 270.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/8gs5 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/8gs5 | HTTPS FTP |
-Related structure data
Related structure data | 8grbC 8grdC 8grgC 8grhC 8gruC 7ce3S 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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1 |
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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.: 8 / Mutation: Q139A 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: 38867.523 Da / Num. of mol.: 4 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: 39152.031 Da / Num. of mol.: 4 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 |
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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: 5.33 Å3/Da / Density % sol: 76.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M NaCl, 0.1 M MES (pH 6.5), and 10% (w/v) PEG 4000 |
-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: Nov 15, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.486→50 Å / Num. obs: 69186 / % possible obs: 89.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.111 / Rrim(I) all: 0.233 / Χ2: 0.903 / Net I/σ(I): 2.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CE3 Resolution: 4.486→30.542 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.04 / 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: 265.48 Å2 / Biso mean: 107.5421 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.486→30.542 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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