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

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Basic information

Entry
Database: PDB / ID: 8grd
TitleCrystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ADP and Mg
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
KeywordsOXIDOREDUCTASE / 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 / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix ...isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / 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
ADENOSINE-5'-DIPHOSPHATE / Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsChen, X. / Sun, P. / 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: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2294
Polymers75,7772
Non-polymers4522
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-44 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.897, 165.897, 129.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial / Isocitric dehydrogenase subunit alpha / NAD(+)-specific ICDH subunit alpha


Mass: 36625.125 Da / Num. of mol.: 1
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 Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / Isocitric dehydrogenase subunit beta / NAD(+)-specific ICDH subunit beta


Mass: 39152.031 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: O43837-2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.1 M sodium cacodylate (pH 5.1), 0.1 M calcium acetate, 10% (w/v) PEG 8000, 4 mM ADP, 4 mM CIT and 0.4 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2021
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.699→50 Å / Num. obs: 25101 / % possible obs: 100 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.029 / Rrim(I) all: 0.152 / Χ2: 0.478 / Net I/σ(I): 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.75261.08612300.9040.2161.1070.43699.9
2.75-2.824.70.96812340.9160.1970.9880.443100
2.8-2.85230.79312430.9320.1680.8110.46100
2.85-2.9125.30.70512260.9560.1420.7190.446100
2.91-2.9728.20.59212390.9730.1130.6030.459100
2.97-3.0428.40.51512330.9750.0980.5240.46100
3.04-3.1228.10.44112470.9820.0840.4490.467100
3.12-3.2280.35312300.9890.0680.360.472100
3.2-3.327.80.31812410.9910.0610.3240.54100
3.3-3.427.70.24812440.9930.0480.2530.482100
3.4-3.5227.20.24512430.9960.0480.2490.582100
3.52-3.6627.20.1912450.9970.0370.1930.524100
3.66-3.8326.40.16612660.9970.0330.1690.58100
3.83-4.0324.70.1412450.9980.0290.1430.566100
4.03-4.2922.60.09112480.9990.0190.0930.483100
4.29-4.6227.70.07612690.9990.0150.0780.461100
4.62-5.0827.70.069126210.0130.0710.447100
5.08-5.8127.20.07912800.9990.0150.0810.435100
5.81-7.3225.20.06813040.9990.0140.070.398100
7.32-5023.50.04213720.9990.0090.0430.414100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDF

6kdf


Resolution: 2.699→23.313 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1248 5.01 %
Rwork0.194 23667 -
obs0.1965 24915 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.4 Å2 / Biso mean: 50.1481 Å2 / Biso min: 25.27 Å2
Refinement stepCycle: final / Resolution: 2.699→23.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 28 54 5094
Biso mean--43.57 47.97 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095123
X-RAY DIFFRACTIONf_angle_d1.0416914
X-RAY DIFFRACTIONf_chiral_restr0.054790
X-RAY DIFFRACTIONf_plane_restr0.006886
X-RAY DIFFRACTIONf_dihedral_angle_d7.8343122
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.699-2.80680.32591350.2474257599
2.8068-2.93430.32411370.24422595100
2.9343-3.08870.3191380.23222606100
3.0887-3.28170.25461370.23042608100
3.2817-3.53430.31481380.22322624100
3.5343-3.88850.2711380.19572612100
3.8885-4.44780.19651380.16822651100
4.4478-5.5910.18921420.15922678100
5.591-23.3130.2051450.1807271897

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