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- PDB-8grg: Crystal structure of a constitutively active mutant of the alpha ... -

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Basic information

Entry
Database: PDB / ID: 8grg
TitleCrystal structure of a constitutively active mutant of the alpha gamma heterodimer of human IDH3
Components
  • Human IDH3 alpha subunit
  • Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
KeywordsOXIDOREDUCTASE / Isocitrate dehydrogenase / IDH3 / 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
Isocitrate dehydrogenase NAD-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial / Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsSun, P. / Chen, X. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870723 China
CitationJournal: 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
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human IDH3 alpha subunit
B: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial


Theoretical massNumber of molelcules
Total (without water)75,4932
Polymers75,4932
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-30 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.513, 73.527, 86.618
Angle α, β, γ (deg.)90.000, 107.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Human IDH3 alpha subunit


Mass: 36625.125 Da / Num. of mol.: 1 / Mutation: Q139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P50213
#2: Protein Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial / NAD-IDH gamma subunit / Isocitric dehydrogenase subunit gamma / NAD(+)-specific ICDH subunit gamma


Mass: 38867.523 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES (pH 6.0) and 20% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2017
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.699→50 Å / Num. obs: 22588 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.049 / Rrim(I) all: 0.132 / Χ2: 1.733 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.87.50.48422240.9470.1890.521.11199.9
2.8-2.917.50.38722280.9570.1510.4161.24899.9
2.91-3.047.50.28922630.9730.1130.311.388100
3.04-3.27.40.21522620.9810.0850.2311.673100
3.2-3.47.50.16922480.9870.0660.1811.919100
3.4-3.667.30.13722550.9850.0550.1472.247100
3.66-4.037.30.11922630.990.0470.1282.239100
4.03-4.627.10.09522690.9920.0390.1021.93399.9
4.62-5.817.40.08722680.9940.0350.0941.81699.9
5.81-507.20.08723080.9920.0360.0941.77798.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRH

5grh


Resolution: 2.699→37.312 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1135 5.03 %
Rwork0.1837 21445 -
obs0.185 22580 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.64 Å2 / Biso mean: 49.7036 Å2 / Biso min: 24.46 Å2
Refinement stepCycle: final / Resolution: 2.699→37.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 0 39 4929
Biso mean---46.31 -
Num. residues----642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.699-2.82150.33771300.2282243892
2.8215-2.97020.28331610.22162686100
2.9702-3.15620.28261340.20872710100
3.1562-3.39980.2351500.19212682100
3.3998-3.74160.21531430.1782719100
3.7416-4.28240.19511310.16992727100
4.2824-5.39270.17011500.16292711100
5.3927-37.3120.16331360.1816277299

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