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- PDB-5yzh: Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 5yzh
TitleCrystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / IDH
Function / homology
Function and homology information


NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / isocitrate metabolic process / Peroxisomal protein import / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle ...NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / isocitrate metabolic process / Peroxisomal protein import / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / glutathione metabolic process / tricarboxylic acid cycle / Neutrophil degranulation / response to organic cyclic compound / peroxisome / NAD binding / NADP binding / response to oxidative stress / magnesium ion binding / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.994 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione.
Authors: Cho, H.J. / Cho, H.Y. / Park, J.W. / Kwon, O.S. / Lee, H.S. / Huh, T.L. / Kang, B.S.
History
DepositionDec 14, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 4, 2018ID: 2CMJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0525
Polymers93,4732
Non-polymers1,5793
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-53 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.372, 91.289, 109.381
Angle α, β, γ (deg.)90.00, 113.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-867-

HOH

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Components

#1: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 46736.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Idh1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O88844, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate pH 5.5,16% PEG 4000 , 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: Bruker AXIOM 200 / Detector: CCD / Date: Nov 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 57456 / % possible obs: 96.2 % / Redundancy: 6.8 % / Net I/σ(I): 44.7
Reflection shellResolution: 1.99→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.994→24.308 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9
RfactorNum. reflection% reflection
Rfree0.2214 2883 5.05 %
Rwork0.1823 --
obs0.1843 57131 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.994→24.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 102 615 7204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046736
X-RAY DIFFRACTIONf_angle_d0.9059094
X-RAY DIFFRACTIONf_dihedral_angle_d16.1782533
X-RAY DIFFRACTIONf_chiral_restr0.034982
X-RAY DIFFRACTIONf_plane_restr0.0041153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.994-2.02650.3945123215480
2.0265-2.06150.3722120233587
2.0615-2.09890.3293113241289
2.0989-2.13930.3213134242691
2.1393-2.18290.2875120246391
2.1829-2.23030.2656138250792
2.2303-2.28220.2794116254793
2.2822-2.33920.2743126249394
2.3392-2.40240.2917140257295
2.4024-2.4730.287158260396
2.473-2.55280.289140262798
2.5528-2.64390.2307151265299
2.6439-2.74960.2509129268299
2.7496-2.87460.23981412723100
2.8746-3.02590.22691442705100
3.0259-3.21510.21621320.17832705100
3.2151-3.46260.21271590.17262712100
3.4626-3.80990.21251530.15332708100
3.8099-4.35850.15191440.13782718100
4.3585-5.48080.16521610.12852728100
5.48080.1571412776100

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