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- PDB-3inm: Crystal structure of human cytosolic NADP(+)-dependent isocitrate... -

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Basic information

Entry
Database: PDB / ID: 3inm
TitleCrystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / NADP / KETOGLUTARATE / QUATERNARY COMPLEX / Glyoxylate bypass / Magnesium / Manganese / Metal-binding / Peroxisome / Tricarboxylic acid cycle
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / glutathione metabolic process / tricarboxylic acid cycle / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / 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
2-OXOGLUTARIC ACID / Chem-NDP / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFontano, E. / Brown, R.S. / Suto, R.K. / Bhyravbhatla, B.
CitationJournal: Nature / Year: 2009
Title: Cancer-associated IDH1 mutations produce 2-hydroxyglutarate.
Authors: Dang, L. / White, D.W. / Gross, S. / Bennett, B.D. / Bittinger, M.A. / Driggers, E.M. / Fantin, V.R. / Jang, H.G. / Jin, S. / Keenan, M.C. / Marks, K.M. / Prins, R.M. / Ward, P.S. / Yen, K.E. ...Authors: Dang, L. / White, D.W. / Gross, S. / Bennett, B.D. / Bittinger, M.A. / Driggers, E.M. / Fantin, V.R. / Jang, H.G. / Jin, S. / Keenan, M.C. / Marks, K.M. / Prins, R.M. / Ward, P.S. / Yen, K.E. / Liau, L.M. / Rabinowitz, J.D. / Cantley, L.C. / Thompson, C.B. / Vander Heiden, M.G. / Su, S.M.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,54718
Polymers144,4073
Non-polymers3,14015
Water5,423301
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,36512
Polymers96,2712
Non-polymers2,09310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-95 kcal/mol
Surface area29720 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules

C: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,36512
Polymers96,2712
Non-polymers2,09310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area12130 Å2
ΔGint-95 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.120, 274.690, 116.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 48135.684 Da / Num. of mol.: 3 / Mutation: R132H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Plasmid: PET-41A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)

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Non-polymers , 6 types, 316 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.67 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride, 10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt. Precipitant: 100mM MES pH 6.5, 20% ...Details: Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride, 10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt. Precipitant: 100mM MES pH 6.5, 20% PEG 6000. Ratio of protein component to precipitant in initial hanging drop: 2:1., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2009 / Details: MIRROR AND MONOCHROMETER
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 89958 / Num. obs: 83121 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.014 / Net I/σ(I): 20.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5232 / Χ2: 1.006 / % possible all: 58.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.61 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å19.99 Å
Translation2.3 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T0L

1t0l


Resolution: 2.1→24.91 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.232 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.881 / SU B: 4.814 / SU ML: 0.125 / SU R Cruickshank DPI: 0.251 / SU Rfree: 0.207 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 4153 5 %RANDOM
Rwork0.22 ---
obs0.222 78956 92.36 %-
all-83109 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.12 Å2 / Biso mean: 33.273 Å2 / Biso min: 15.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9706 0 198 301 10205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210111
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.96813661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85851222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82524.848460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.723151787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2261542
X-RAY DIFFRACTIONr_chiral_restr0.090.21466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217556
X-RAY DIFFRACTIONr_mcbond_it0.6981.56059
X-RAY DIFFRACTIONr_mcangle_it1.31829748
X-RAY DIFFRACTIONr_scbond_it2.32134052
X-RAY DIFFRACTIONr_scangle_it3.7744.53913
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 208 -
Rwork0.316 3417 -
all-3625 -
obs-3625 55.68 %

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